From 51c60902fae1c72f52f214f59ee37e91e77ef691 Mon Sep 17 00:00:00 2001 From: Mikko Nieminen Date: Fri, 12 May 2023 12:37:54 +0200 Subject: [PATCH 01/14] add cubi-isa-templates dependency, remove local templates (#96) --- cubi_tk/archive/readme.py | 3 +- cubi_tk/isa_tpl/__init__.py | 125 +----------------- .../isatab-bulk_rnaseq/cookiecutter.json | 17 --- ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 5 - .../i_Investigation.txt | 95 ------------- .../s_{{cookiecutter.s_file_name}}.txt | 5 - .../isa_tpl/isatab-generic/cookiecutter.json | 58 -------- ....~lock.s_{{cookiecutter.s_file_name}}.txt# | 1 - ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 5 - .../i_Investigation.txt | 93 ------------- .../s_{{cookiecutter.s_file_name}}.txt | 5 - .../isa_tpl/isatab-germline/cookiecutter.json | 74 ----------- ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 5 - .../i_Investigation.txt | 95 ------------- .../s_{{cookiecutter.s_file_name}}.txt | 5 - .../isatab-microarray/cookiecutter.json | 41 ------ ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 5 - .../i_investigation.txt | 95 ------------- .../s_{{cookiecutter.s_file_name}}.txt | 5 - .../cookiecutter.json | 81 ------------ ...efix}}_{{cookiecutter.assay_name}}_FIA.txt | 6 - ...refix}}_{{cookiecutter.assay_name}}_LC.txt | 6 - .../i_Investigation.txt | 95 ------------- .../s_{{cookiecutter.study_file_name}}.txt | 6 - .../cookiecutter.json | 35 ----- ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 14 -- .../i_Investigation.txt | 100 -------------- .../s_{{cookiecutter.s_file_name}}.txt | 7 - .../isatab-stem_cell_core/cookiecutter.json | 20 --- ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 8 -- .../i_Investigation.txt | 100 -------------- .../s_{{cookiecutter.s_file_name}}.txt | 7 - .../cookiecutter.json | 20 --- ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 7 - .../i_Investigation.txt | 99 -------------- .../s_{{cookiecutter.s_file_name}}.txt | 7 - .../cookiecutter.json | 39 ------ ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 15 --- .../i_Investigation.txt | 100 -------------- .../s_{{cookiecutter.s_file_name}}.txt | 8 -- .../isatab-tumor_normal_dna/cookiecutter.json | 1 - ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 1 - .../i_Investigation.txt | 1 - .../s_{{cookiecutter.s_file_name}}.txt | 1 - .../cookiecutter.json | 72 ---------- ...iptome_profiling_nucleotide_sequencing.txt | 5 - ...y_prefix}}_{{cookiecutter.assay_name}}.txt | 5 - .../i_Investigation.txt | 95 ------------- .../s_{{cookiecutter.s_file_name}}.txt | 5 - requirements/base.txt | 3 + setup.py | 6 +- 51 files changed, 14 insertions(+), 1698 deletions(-) delete mode 100644 cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-generic/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/.~lock.s_{{cookiecutter.s_file_name}}.txt# delete mode 100644 cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-germline/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/i_investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt delete mode 100644 cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt delete mode 100644 cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 120000 cubi_tk/isa_tpl/isatab-tumor_normal_dna/cookiecutter.json delete mode 120000 cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 120000 cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 120000 cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json delete mode 100644 cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt delete mode 100644 cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt delete mode 100644 cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/i_Investigation.txt delete mode 100644 cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt diff --git a/cubi_tk/archive/readme.py b/cubi_tk/archive/readme.py index 409d1456..976f2a17 100644 --- a/cubi_tk/archive/readme.py +++ b/cubi_tk/archive/readme.py @@ -12,11 +12,12 @@ import attr from cookiecutter.main import cookiecutter +from cubi_isa_templates import IsaTabTemplate from logzero import logger from . import common from ..common import execute_shell_commands -from ..isa_tpl import IsaTabTemplate + _TEMPLATE_DIR = os.path.join(os.path.dirname(__file__), "templates") diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py index cbfa7c68..44ae7eff 100644 --- a/cubi_tk/isa_tpl/__init__.py +++ b/cubi_tk/isa_tpl/__init__.py @@ -18,29 +18,12 @@ Available Templates ------------------- -The `Cookiecutter`_ directories are located in this module's directory. Currently available templates are: - -- ``isatab-generic`` -- ``isatab-germline`` -- ``isatab-microarray`` -- ``isatab-ms_meta_biocrates`` -- ``isatab-single_cell_rnaseq`` -- ``isatab-bulk_rnaseq`` -- ``isatab-tumor_normal_dna`` -- ``isatab-tumor_normal_triplets`` -- ``isatab-stem_cell_core_bulk`` -- ``isatab-stem_cell_core_sc`` +These have been moved to a separate repository: see `cubi-isa-templates`_. Adding Templates ---------------- -Adding templates consists of the following steps: - -1. Add a new template directory below ``cubi_tk/isa_tpl``. -2. Register it appending a ``IsaTabTemplate`` object to ``_TEMPLATES`` in ``cubi_tk.isa_tpl``. -3. Add it to the list above in the docstring. - -The easiest way to start out is to copy an existing cookiecutter template and registration. +See `cubi-isa-templates`_. More Information ---------------- @@ -48,122 +31,22 @@ Also see ``cubi-tk isa-tpl`` CLI documentation and ``cubi-tk isa-tab --help`` for more information. .. _Cookiecutter: https://cookiecutter.readthedocs.io/ +.. _cubi-isa-templates: https://github.com/bihealth/cubi-isa-templates """ import argparse from functools import partial -import json import os from pathlib import Path -import typing -import attr from cookiecutter.main import cookiecutter +from cubi_isa_templates import TEMPLATES from logzero import logger from toolz import curry from ..common import run_nocmd, yield_files_recursively -@attr.s(frozen=True, auto_attribs=True) -class IsaTabTemplate: - """Information regarding an ISA-tab template.""" - - #: Name of the ISA-tab template. - name: str - - #: Path to template directory. - path: str - - #: Configuration loaded from ``cookiecutter.json``. - configuration: typing.Dict[str, typing.Any] - - #: Optional description string. - description: typing.Optional[str] = None - - -#: Base directory to this file. -_BASE_DIR = os.path.dirname(__file__) - - -def load_variables(template_name, extra=None): - """Load variables given the template name.""" - extra = extra or {} - config_path = os.path.join(_BASE_DIR, template_name, "cookiecutter.json") - with open(config_path, "rt") as inputf: - result = json.load(inputf) - result.update(extra) - return result - - -#: Known ISA-tab templates (internal, mapping generated below). -_TEMPLATES = ( - IsaTabTemplate( - name="single_cell_rnaseq", - path=os.path.join(_BASE_DIR, "isatab-single_cell_rnaseq"), - description="single cell RNA sequencing ISA-tab template", - configuration=load_variables("isatab-single_cell_rnaseq"), - ), - IsaTabTemplate( - name="bulk_rnaseq", - path=os.path.join(_BASE_DIR, "isatab-bulk_rnaseq"), - description="bulk RNA sequencing ISA-tab template", - configuration=load_variables("isatab-generic"), - ), - IsaTabTemplate( - name="tumor_normal_dna", - path=os.path.join(_BASE_DIR, "isatab-tumor_normal_dna"), - description="Tumor-Normal DNA sequencing ISA-tab template", - configuration=load_variables("isatab-tumor_normal_dna", {"is_triplet": False}), - ), - IsaTabTemplate( - name="tumor_normal_triplets", - path=os.path.join(_BASE_DIR, "isatab-tumor_normal_triplets"), - description="Tumor-Normal DNA+RNA sequencing ISA-tab template", - configuration=load_variables("isatab-tumor_normal_triplets", {"is_triplet": True}), - ), - IsaTabTemplate( - name="germline", - path=os.path.join(_BASE_DIR, "isatab-germline"), - description="germline DNA sequencing ISA-tab template", - configuration=load_variables("isatab-germline"), - ), - IsaTabTemplate( - name="generic", - path=os.path.join(_BASE_DIR, "isatab-generic"), - description="generic RNA sequencing ISA-tab template", - configuration=load_variables("isatab-generic"), - ), - IsaTabTemplate( - name="microarray", - path=os.path.join(_BASE_DIR, "isatab-microarray"), - description="microarray ISA-tab template", - configuration=load_variables("isatab-microarray"), - ), - IsaTabTemplate( - name="ms_meta_biocrates", - path=os.path.join(_BASE_DIR, "isatab-ms_meta_biocrates"), - description="MS Metabolomics Biocrates kit ISA-tab template", - configuration=load_variables("isatab-ms_meta_biocrates"), - ), - IsaTabTemplate( - name="stem_cell_core_bulk", - path=os.path.join(_BASE_DIR, "isatab-stem_cell_core_bulk"), - description="Bulk RNA sequencing ISA-tab template from hiPSC for stem cell core projects", - configuration=load_variables("isatab-stem_cell_core_bulk"), - ), - IsaTabTemplate( - name="stem_cell_core_sc", - path=os.path.join(_BASE_DIR, "isatab-stem_cell_core_sc"), - description="Single cell RNA sequencing ISA-tab template from hiPSC for stem cell core projects", - configuration=load_variables("isatab-stem_cell_core_sc"), - ), -) - -#: Known ISA-tab templates. -TEMPLATES = {tpl.name: tpl for tpl in _TEMPLATES} - - @curry def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False): """Run cookiecutter, ``tpl`` will be bound with ``toolz.curry``.""" diff --git a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json b/cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json deleted file mode 100644 index d3c0f735..00000000 --- a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/cookiecutter.json +++ /dev/null @@ -1,17 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "sample1,sample2", - "a_measurement_type": [ - "transcription profiling" - ], - "instrument": "Illumina NextSeq 500", - "center_name": "", - "center_contact": "", - - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "nucleotide sequencing", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index ba01e134..00000000 --- a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration] Performer Date Protocol REF Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode name] Performer Date Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Base quality encoding] Parameter Value[Library prefix] Performer Date Library Name -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} RNA extraction Library construction Nucleic acid sequencing {{sample_name}} {{sample_name}} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 76366d47..00000000 --- a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_bulk_RNAseq -Comment[Last Opened With Configuration] bih_bulk_RNAseq -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -Study Protocol Name Sample collection RNA extraction Library construction Nucleic acid sequencing -Study Protocol Type Sample collection RNA extraction Library construction Nucleic acid sequencing -Study Protocol Type Term Accession Number "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" -Study Protocol Description "" "" "" "" -Study Protocol URI "" "" "" "" -Study Protocol Version "" "" "" "" -Study Protocol Parameters Name Method Concentration Library source;Library strategy;Library selection;Library layout;Library kit;Target insert size;Wet-lab insert size;Barcode kit;Barcode name Platform;Instrument model;Base quality encoding;Library prefix -Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;" ";;;" -Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;" ";;;" -Study Protocol Components Name "" "" "" "" -Study Protocol Components Type "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index db09f51d..00000000 --- a/cubi_tk/isa_tpl/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Source type] Characteristics[external reference] Characteristics[Group] Protocol REF Parameter Value[Method] Performer Date Sample Name Characteristics[Origin] Characteristics[Condition] Characteristics[Treatment] -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 Sample collection {{sample_name|replace("-", "_")}} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-generic/cookiecutter.json b/cubi_tk/isa_tpl/isatab-generic/cookiecutter.json deleted file mode 100644 index dddd96d7..00000000 --- a/cubi_tk/isa_tpl/isatab-generic/cookiecutter.json +++ /dev/null @@ -1,58 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "alpha,beta,gamma", - "a_measurement_type": [ - "transcription profiling" - ], - "a_measurement_types": { - "transcription profiling" : { - "accession" : "http://purl.obolibrary.org/obo/OBI_0000424", - "source" : "OBI" - } - }, - "a_technology_type": "nucleotide sequencing", - "a_technology_types": { - "nucleotide sequencing" : { - "accession" : "http://purl.obolibrary.org/obo/OBI_0000626", - "source" : "OBI" - } - }, - - "lib_kit": [ - "Illumina TruSeq Stranded mRNA" - ], - "organism": [ - "Homo sapiens", - "Mus musculus" - ], - "batch": "1", - "lib_kits": { - "Illumina TruSeq Stranded mRNA": { - "name": "Illumina TruSeq Stranded mRNA" - } - }, - "organisms": { - "Homo sapiens": { - "name": "Homo sapiens", - "taxon": "9606" - }, - "Mus musculus": { - "name": "Mus musculus", - "taxon": "10090" - } - }, - "instrument": "Illumina NovaSeq 6000", - "center_name": "", - "center_contact": "", - - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'transcription profiling' %}mRNA_seq{% else %}UNKNOWN{% endif %}", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "sample_type": "x-charite-medgen-blood-book-id", - "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}RNA-seq{% else %}UNKNOWN{% endif %}", - "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'mRNA_seq' %}PolyA{% else %}UNKNOWN{% endif %}", - "lib_layout": [ "PAIRED", "SINGLE" ], - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/.~lock.s_{{cookiecutter.s_file_name}}.txt# b/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/.~lock.s_{{cookiecutter.s_file_name}}.txt# deleted file mode 100644 index 700e15fe..00000000 --- a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/.~lock.s_{{cookiecutter.s_file_name}}.txt# +++ /dev/null @@ -1 +0,0 @@ -Manuel Holtgrewe,mholtgre,cubi16.bihealth.org,12.10.2019 17:49,file:///home/mholtgre/.config/libreoffice/4; \ No newline at end of file diff --git a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index 6bdd8603..00000000 --- a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Extract Name Characteristics[Folder name] Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date Raw Data File Library Name -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{sample_name|replace("-", "_")}}-N1-RNA1 Library construction {{cookiecutter.a_measurement_abbreviation}} TRANSCRIPTOMIC {{cookiecutter.lib_strategy}} {{cookiecutter.lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kits[cookiecutter.lib_kit].name}} {{sample_name|replace("-", "_")}}-N1-RNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{sample_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 {{sample_name|replace("-", "_")}} -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 5eff93e2..00000000 --- a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,93 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA CL -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO http://data.bioontology.org/ontologies/CL -Term Source Version 48 35 10 12 570 2.8 2019-08-12 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology Cell Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number {{cookiecutter.a_measurement_types[cookiecutter.a_measurement_type].accession}} -Study Assay Measurement Type Term Source REF {{cookiecutter.a_measurement_types[cookiecutter.a_measurement_type].source}} -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number {{cookiecutter.a_technology_types[cookiecutter.a_technology_type].accession}} -Study Assay Technology Type Term Source REF {{cookiecutter.a_technology_types[cookiecutter.a_technology_type].source}} -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -Study Protocol Name Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} -Study Protocol Type Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} -Study Protocol Type Term Accession Number "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" -Study Protocol Description "" "" "" "" -Study Protocol URI "" "" "" "" -Study Protocol Version "" "" "" "" -Study Protocol Parameters Name "" Concentration measurement "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Barcode name;Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Instrument model;Center name" -Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;" -Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;" -Study Protocol Components Name "" "" "" "" -Study Protocol Components Type "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 2a53e222..00000000 --- a/cubi_tk/isa_tpl/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[External links] Characteristics[Batch] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[Disease status] Characteristics[OMIM disease] Term Source REF Term Accession Number Characteristics[Orphanet disease] Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Sample Name Characteristics[External links] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} {{cookiecutter.sample_type}}:{{sample_name}} {{cookiecutter.batch}} {{cookiecutter.organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}} UNKNOWN UNKNOWN Sample collection {{sample_name|replace("-", "_")}}-N1 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-germline/cookiecutter.json b/cubi_tk/isa_tpl/isatab-germline/cookiecutter.json deleted file mode 100644 index a0296018..00000000 --- a/cubi_tk/isa_tpl/isatab-germline/cookiecutter.json +++ /dev/null @@ -1,74 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "index,mother,father", - "a_measurement_type": [ - "exome sequencing", - "genome sequencing", - "panel sequencing" - ], - "lib_kit": [ - "Agilent SureSelect Human All Exon V8", - "Agilent SureSelect Human All Exon V7", - "Agilent SureSelect Human All Exon V6r2", - "Agilent SureSelect Human All Exon V5", - "Agilent SureSelect Human All Exon V4", - "IDT xGen Exome Research Panel V1.0", - "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "Illumina TruSeq PCR-free", - "Illumina TruSeq Nano" - ], - "batch": "1", - "lib_kits": { - "Agilent SureSelect Human All Exon V8": { - "name": "Agilent SureSelect Human All Exon V8", - "cat_id": "S33266436" - }, - "Agilent SureSelect Human All Exon V6r2": { - "name": "Agilent SureSelect Human All Exon V6r2", - "cat_id": "S04380110" - }, - "Agilent SureSelect Human All Exon V5": { - "name": "Agilent SureSelect Human All Exon V5", - "cat_id": "S04380110" - }, - "Agilent SureSelect Human All Exon V4": { - "name": "Agilent SureSelect Human All Exon V4", - "cat_id": "S03723314" - }, - "Agilent SureSelect Human All Exon V7": { - "name": "Agilent SureSelect Human All Exon V7", - "cat_id": "S31285117" - }, - "IDT xGen Exome Research Panel V1.0": { - "name": "IDT xGen Exome Research Panel V1.0", - "cat_id": "" - }, - "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in": { - "name": "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "cat_id": "" - }, - "Illumina TruSeq PCR-free": { - "name": "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "cat_id": "" - }, - "Illumina TruSeq Nano": { - "name": "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "cat_id": "" - } - }, - "instrument": "Illumina NextSeq 500", - "center_name": "", - "center_contact": "", - - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "nucleotide sequencing", - "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'exome sequencing' %}WES{% else %}WGS{% endif %}", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "sample_type": "x-charite-medgen-blood-book-id", - "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}WXS{% else %}WGS{% endif %}", - "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}Hybrid Selection{% else %}RANDOM{% endif %}", - "lib_layout": "PAIRED", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index 365d1f70..00000000 --- a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Library Name Characteristics[Folder name] Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date Raw Data File -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{sample_name|replace("-", "_")}}-N1-DNA1 Library construction {{cookiecutter.a_measurement_abbreviation}} GENOMIC {{cookiecutter.lib_strategy}} {{cookiecutter.lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kits[cookiecutter.lib_kit].name}} {{cookiecutter.lib_kits[cookiecutter.lib_kit].cat_id}} {{sample_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{sample_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 6db9900c..00000000 --- a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_germline -Comment[Last Opened With Configuration] bih_germline -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number "" -Study Assay Measurement Type Term Source REF "" -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -Study Protocol Name Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} -Study Protocol Type Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} -Study Protocol Type Term Accession Number "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" -Study Protocol Description "" "" "" "" -Study Protocol URI "" "" "" "" -Study Protocol Version "" "" "" "" -Study Protocol Parameters Name "" Concentration measurement "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Barcode name;Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Instrument model;Center name" -Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;" -Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;" -Study Protocol Components Name "" "" "" "" -Study Protocol Components Type "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 743a7872..00000000 --- a/cubi_tk/isa_tpl/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[External links] Characteristics[Batch] Characteristics[Family] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Mother] Characteristics[Father] Comment[Family notes] Characteristics[Sex] Characteristics[Disease status] Characteristics[OMIM disease] Term Source REF Term Accession Number Characteristics[Orphanet disease] Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Sample Name Characteristics[External links] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} {{cookiecutter.sample_type}}:{{sample_name}} {{cookiecutter.batch}} FAM_{{sample_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 0 0 UNKNOWN UNKNOWN Sample collection {{sample_name|replace("-", "_")}}-N1 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json b/cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json deleted file mode 100644 index 55579b41..00000000 --- a/cubi_tk/isa_tpl/isatab-microarray/cookiecutter.json +++ /dev/null @@ -1,41 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "alpha,beta,gamma", - "a_measurement_type": [ - "transcription profiling" - ], - "organism": [ - "Homo sapiens", - "Mus musculus" - ], - "organisms": { - "Homo sapiens": { - "name": "Homo sapiens", - "taxon": "9606" - }, - "Mus musculus": { - "name": "Mus musculus", - "taxon": "10090" - } - }, - "technology_platform": "Illumina BeadChip", - "array_design_ref": "", - - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "microarray", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - - "terms": { - "transcription profiling": { - "accession_number": "http://purl.obolibrary.org/obo/OBI_0000424", - "source_ref": "OBI" - }, - "microarray": { - "accession_number": "http://purl.obolibrary.org/obo/OBI_0400148", - "source_ref": "OBI" - } - }, - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index d47c8fc3..00000000 --- a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Performer Date Extract Name Protocol REF Performer Date Labeled Extract Name Label Protocol REF Performer Date Hybridization Assay Name Array Design REF Protocol REF Performer Date Scan Name Image File Array Data File Array Data Matrix File Protocol REF Performer Date Normalization Name Derived Array Data File Protocol REF Performer Date Data Transformation Name Derived Array Data Matrix File -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-S1 Nucleic acid extraction {{sample_name|replace("-", "_")}}-S1-E1 Labeling Nucleic acid hybridization {{sample_name|replace("-", "_")}}-S1-E1-H1 {{cookiecutter.array_design_ref}} Data collection {{sample_name|replace("-", "_")}}-S1-E1-H1 Normalization data transformation Data transformation -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/i_investigation.txt b/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/i_investigation.txt deleted file mode 100644 index 1e5079a6..00000000 --- a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/i_investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name PATO OBI NCBITAXON -Term Source File http://data.bioontology.org/ontologies/PATO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON -Term Source Version 1.2 31 8 -Term Source Description Phenotype And Trait Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] "" -Comment[Last Opened With Configuration] "" -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type "" -Study Design Type Term Accession Number "" -Study Design Type Term Source REF "" -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name "" -Study Factor Type "" -Study Factor Type Term Accession Number "" -Study Factor Type Term Source REF "" -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number {{cookiecutter.terms[cookiecutter.a_measurement_type].accession_number}} -Study Assay Measurement Type Term Source REF {{cookiecutter.terms[cookiecutter.a_measurement_type].source_ref}} -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number {{cookiecutter.terms[cookiecutter.a_technology_type].accession_number}} -Study Assay Technology Type Term Source REF {{cookiecutter.terms[cookiecutter.a_technology_type].source_ref}} -Study Assay Technology Platform {{cookiecutter.technology_platform}} -STUDY PROTOCOLS -Study Protocol Name Sample collection Nucleic acid extraction Labeling Nucleic acid hybridization Data collection Normalization data transformation Data transformation -Study Protocol Type sample collection nucleic acid extraction Labeling nucleic acid hybridization data collection normalization data transformation data transformation -Study Protocol Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0666667 http://purl.obolibrary.org/obo/OBI_0302903 -Study Protocol Type Term Source REF OBI OBI -Study Protocol Description "" "" "" "" "" "" "" -Study Protocol URI "" "" "" "" "" "" "" -Study Protocol Version "" "" "" "" "" "" "" -Study Protocol Parameters Name "" "" "" "" "" "" "" -Study Protocol Parameters Name Term Accession Number "" "" "" "" "" "" "" -Study Protocol Parameters Name Term Source REF "" "" "" "" "" "" "" -Study Protocol Components Name "" "" "" "" "" "" "" -Study Protocol Components Type "" "" "" "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 811684b5..00000000 --- a/cubi_tk/isa_tpl/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[Organism] Term Source REF Term Accession Number Protocol REF Performer Date Sample Name Factor Value[time of differentiation] Unit Term Source REF Term Accession Number -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} {{cookiecutter.organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}} Sample collection {{sample_name|replace("-", "_")}}-S1 day OBI http://purl.obolibrary.org/obo/UO_0000033 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json deleted file mode 100644 index 318a6b1c..00000000 --- a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/cookiecutter.json +++ /dev/null @@ -1,81 +0,0 @@ -{ - "investigation_title": "Investigation Title", - - "study_title": "{{cookiecutter.investigation_title}}", - "study_id": "{{cookiecutter.study_title|lower|replace(' ', '_')}}", - "study_file_name": "{{cookiecutter.study_id}}", - - "sample_names": "alpha,beta,gamma", - - "organism": [ - "Homo sapiens", - "Mus musculus" - ], - "organisms": { - "Homo sapiens": { - "name": "Homo sapiens", - "taxon": "9606" - }, - "Mus musculus": { - "name": "Mus musculus", - "taxon": "10090" - } - }, - - "assay_measurement_type": [ - "metabolite profiling" - ], - "assay_technology_type": [ - "mass spectrometry" - ], - "assay_technology_types": { - "mass spectrometry": { - "term": "mass spectrometry", - "source": "OBI", - "accession": "http://purl.obolibrary.org/obo/OBI_0000470" - } - }, - - "biocrates_kit": [ - "Biocrates MxP Quant 500 Kit", - "Biocrates AbsoluteIDQ p400 HR Kit" - ], - - "assay_prefix": "{{cookiecutter.study_id}}", - "assay_name": "{{cookiecutter.biocrates_kit|replace(' ', '_')}}", - "assay_measurement_abbreviation_LC": "B-LC", - "assay_measurement_abbreviation_FIA": "B-FIA", - - "biocrates_metidq_version": [ - "", - "7.13.11-DB109-Nitrogen-2850" - ], - "metaquac_version": [ - "", - "v0.1.1", - "v0.1.30" - ], - - "instrument": [ - "Sciex 5500", - "TSQ Quantiva" - ], - "instruments": { - "Sciex 5500": { - "term": "QTRAP 5500", - "source": "MS", - "accession": "http://purl.obolibrary.org/obo/MS_1000931" - }, - "TSQ Quantiva": { - "term": "TSQ Quantiva", - "source": "MS", - "accession": "http://purl.obolibrary.org/obo/MS_1002418" - } - }, - - "chromatography_instrument": [ - "Agilent UHPLC 1290", - "Agilent 1290 Infinity II LC System" - ], - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt deleted file mode 100644 index 5cc8e4a7..00000000 --- a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt +++ /dev/null @@ -1,6 +0,0 @@ -Sample Name Protocol REF Parameter Value[Post extraction] Parameter Value[Derivatization] Parameter Value[Phase] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Performer Date Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Term Source REF Term Accession Number Parameter Value[Ion source] Term Source REF Term Accession Number Parameter Value[Mass analyzer] Term Source REF Term Accession Number Parameter Value[Detector] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software name] Parameter Value[Aquisition software version] Parameter Value[Aquisition parameter] Performer Date MS Assay Name Raw Spectral Data File Comment[Batch] Comment[Well position] Comment[Sample type] Protocol REF Parameter Value[Analysis software name] Parameter Value[Analysis software version] Metabolite Assignment File Protocol REF Parameter Value[Software name] Parameter Value[Software version] Parameter Value[Report file] Performer Date -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} {{sample_name|replace("-", "_")}}-N1-Meta1 Flow Injection Analysis {{cookiecutter.assay_measurement_abbreviation_FIA}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_FIA}} {{cookiecutter.instruments[cookiecutter.instrument].term}} {{cookiecutter.instruments[cookiecutter.instrument].source}} {{cookiecutter.instruments[cookiecutter.instrument].accession}} {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_FIA}}1 Data transformation {{cookiecutter.assay_measurement_abbreviation_FIA}} Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control {{cookiecutter.assay_measurement_abbreviation_FIA}} MeTaQuaC {{cookiecutter.metaquac_version}} -{% endfor %} - diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt deleted file mode 100644 index 50060ff4..00000000 --- a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt +++ /dev/null @@ -1,6 +0,0 @@ -Sample Name Protocol REF Parameter Value[Post extraction] Parameter Value[Derivatization] Parameter Value[Phase] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Chromatography instrument] Term Source REF Term Accession Number Parameter Value[Column model] Term Source REF Term Accession Number Parameter Value[Column type] Term Source REF Term Accession Number Performer Date Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Term Source REF Term Accession Number Parameter Value[Ion source] Term Source REF Term Accession Number Parameter Value[Mass analyzer] Term Source REF Term Accession Number Parameter Value[Detector] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software name] Parameter Value[Aquisition software version] Parameter Value[Aquisition parameter] Performer Date MS Assay Name Raw Spectral Data File Comment[Batch] Comment[Well position] Comment[Sample type] Protocol REF Parameter Value[Analysis software name] Parameter Value[Analysis software version] Metabolite Assignment File Protocol REF Parameter Value[Software name] Parameter Value[Software version] Parameter Value[Report file] Performer Date -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} {{sample_name|replace("-", "_")}}-N1-Meta1 Chromatography {{cookiecutter.assay_measurement_abbreviation_LC}} {{cookiecutter.chromatography_instrument}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_LC}} {{cookiecutter.instruments[cookiecutter.instrument].term}} {{cookiecutter.instruments[cookiecutter.instrument].source}} {{cookiecutter.instruments[cookiecutter.instrument].accession}} {{sample_name|replace("-", "_")}}-N1-Meta1-{{cookiecutter.assay_measurement_abbreviation_LC}}1 Data transformation {{cookiecutter.assay_measurement_abbreviation_LC}} Biocrates MetIDQ {{cookiecutter.biocrates_metidq_version}} Quality Control {{cookiecutter.assay_measurement_abbreviation_LC}} MeTaQuaC {{cookiecutter.metaquac_version}} -{% endfor %} - diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 1a5b96a9..00000000 --- a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA CL MS -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO http://data.bioontology.org/ontologies/CL http://data.bioontology.org/ontologies/MS -Term Source Version 48 35 10 12 570 2.8 2019-08-12 122 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology Cell Ontology Mass Spectrometry Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_ms_meta_biocrates -Comment[Last Opened With Configuration] bih_ms_meta_biocrates -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.study_id}} -Study Title {{cookiecutter.study_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.study_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt -Study Assay Measurement Type {{cookiecutter.assay_measurement_type}} {{cookiecutter.assay_measurement_type}} -Study Assay Measurement Type Term Accession Number "" "" -Study Assay Measurement Type Term Source REF "" "" -Study Assay Technology Type {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].term}} {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].term}} -Study Assay Technology Type Term Accession Number {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].accession}} {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].accession}} -Study Assay Technology Type Term Source REF {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].source}} {{cookiecutter.assay_technology_types[cookiecutter.assay_technology_type].source}} -Study Assay Technology Platform {{cookiecutter.biocrates_kit}} {{cookiecutter.biocrates_kit}} -STUDY PROTOCOLS -Study Protocol Name Sample collection Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} Labeling {{cookiecutter.assay_measurement_abbreviation_LC}} Chromatography {{cookiecutter.assay_measurement_abbreviation_LC}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_LC}} Data transformation {{cookiecutter.assay_measurement_abbreviation_LC}} Quality Control {{cookiecutter.assay_measurement_abbreviation_LC}} Extraction {{cookiecutter.assay_measurement_abbreviation_FIA}} Labeling {{cookiecutter.assay_measurement_abbreviation_FIA}} Flow Injection Analysis {{cookiecutter.assay_measurement_abbreviation_FIA}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_FIA}} Data transformation {{cookiecutter.assay_measurement_abbreviation_FIA}} Quality Control {{cookiecutter.assay_measurement_abbreviation_FIA}} -Study Protocol Type Sample collection Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} Labeling {{cookiecutter.assay_measurement_abbreviation_LC}} Chromatography {{cookiecutter.assay_measurement_abbreviation_LC}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_LC}} Data transformation {{cookiecutter.assay_measurement_abbreviation_LC}} Quality Control {{cookiecutter.assay_measurement_abbreviation_LC}} Extraction {{cookiecutter.assay_measurement_abbreviation_FIA}} Labeling {{cookiecutter.assay_measurement_abbreviation_FIA}} Flow Injection Analysis {{cookiecutter.assay_measurement_abbreviation_FIA}} Mass spectrometry {{cookiecutter.assay_measurement_abbreviation_FIA}} Data transformation {{cookiecutter.assay_measurement_abbreviation_FIA}} Quality Control {{cookiecutter.assay_measurement_abbreviation_FIA}} -Study Protocol Type Term Accession Number -Study Protocol Type Term Source REF -Study Protocol Description -Study Protocol URI -Study Protocol Version -Study Protocol Parameters Name Phase;Derivatization;Post extraction Column type;Chromatography instrument;Column model Scan polarity;Mass analyzer;Detector;Aquisition software name;Ion source;Aquisition mode;Instrument;Aquisition parameter;Aquisition software version;Scan m/z range Analysis software name;Analysis software version Report file;Software name;Software version Phase;Derivatization;Post extraction Scan polarity;Mass analyzer;Detector;Aquisition software name;Ion source;Aquisition mode;Instrument;Aquisition parameter;Aquisition software version;Scan m/z range Analysis software name;Analysis software version Report file;Software name;Software version -Study Protocol Parameters Name Term Accession Number ;; ;; ;;;;;;;;; ; ;; ;; ;;;;;;;;; ; ;; -Study Protocol Parameters Name Term Source REF ;; ;; ;;;;;;;;; ; ;; ;; ;;;;;;;;; ; ;; -Study Protocol Components Name -Study Protocol Components Type -Study Protocol Components Type Term Accession Number -Study Protocol Components Type Term Source REF -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt b/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt deleted file mode 100644 index 74e870a6..00000000 --- a/cubi_tk/isa_tpl/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt +++ /dev/null @@ -1,6 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[Disease type] Term Source REF Term Accession Number Characteristics[Disease status] Term Source REF Term Accession Number Characteristics[Age] Unit Term Source REF Term Accession Number Characteristics[BMI] Unit Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Date Sample Name Characteristics[External links] Characteristics[Visit] Characteristics[Visit Centrum] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} {{cookiecutter.organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}} UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection {{sample_name|replace("-", "_")}}-N1 -{% endfor %} - diff --git a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json b/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json deleted file mode 100644 index a9b0842e..00000000 --- a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/cookiecutter.json +++ /dev/null @@ -1,35 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "sample1,sample2", - "a_measurement_type": "transcription profiling", - "lib_kit": [ - "SC3Pv3", - "SC3Pv2", - "SC5P-PE", - "SC5P-R2", - "threeprime", - "fiveprime" - ], - "source_meta": "Source type,External reference,Group", - "sample_meta": "Origin,Condition,Treatment", - "dissociation_meta": "Removal debris,Removal dead cell,Removal ab cell,Cell fixation,Cell viability", - "library_construction_meta": "RNA amount,QC cell load recovery,QC tape fragment size", - "sequencing_meta": "Instrument model,Sequencing parameters", - "_library_types": { - "GEX": {"full" : "Gene Expression", "short": "GEX"}, - "antibody": {"full" : "Antibody Capture", "short": "surface"}, - "VDJ": {"full" : "VDJ-T", "short": "TCR"}, - "other": {"full" : "other", "short": "XXX"}, - "another": {"full" : "foobar", "short": "YYY"}, - "CellPlex": {"full": "Multiplexing Capture", "short": "MPX"} - }, - "library_type": ["GEX", "GEX+antibody", "GEX+VDJ", "GEX+other", "GEX+antibody+VDJ", "GEX+other+another"], - "sample_multiplexing": ["No", "CellPlex", "TotalSeq", "Other"], - "genotype_multiplexing": ["no", "yes"], - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "nucleotide sequencing", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index d0114969..00000000 --- a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,14 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set features = cookiecutter.library_type.split("+") -%} -{% if cookiecutter.sample_multiplexing == "CellPlex" -%}{{ features.append("CellPlex") or "" }}{% endif -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Sample Name Protocol REF Parameter Value[Dissociation method] Parameter Value[Cell count]{%+ for meta in dissociation_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Library kit] Parameter Value[Library type] Parameter Value[Multiplex genotype] Parameter Value[Multiplex sample] Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Extract Name Protocol REF Parameter Value[Sequencing batch] Parameter Value[Fastq prefix] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name -{% for sample_name in sample_names -%} -{% for f_name in features -%} -{% set feature = cookiecutter._library_types[f_name].full -%} -{% set abr = cookiecutter._library_types[f_name].short -%} -{{sample_name|replace("-", "_")}} Dissociation {%+ for meta in dissociation_meta %} {% endfor %} Library construction {{cookiecutter.lib_kit}} {{feature}} {{cookiecutter.genotype_multiplexing == 'yes'}} {{cookiecutter.sample_multiplexing}} {%+ for meta in library_construction_meta %} {% endfor %} {{sample_name}}_{{abr}} Nucleic acid sequencing {{sample_name}}_{{abr}} {%+ for meta in sequencing_meta %} {% endfor %} {{sample_name}} -{% endfor -%} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index c3ffba53..00000000 --- a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,100 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] bih_cancer -Comment[Last Opened With Configuration] bih_cancer -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -{% set source_meta = cookiecutter.source_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Study Protocol Name Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type Term Accession Number "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" -Study Protocol Description "" "" "" "" -Study Protocol URI "" "" "" "" -Study Protocol Version "" "" "" "" -Study Protocol Parameters Name Method Dissociation method;Cell count{% for meta in dissociation_meta -%};{{meta}}{% endfor %} Library kit;Library type;Multiplex genotype;Multiplex sample;Multiplex oligo{% for meta in library_construction_meta -%};{{meta}}{% endfor %} Sequencing batch;Library prefix;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %} -Study Protocol Parameters Name Term Accession Number "" ";{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Parameters Name Term Source REF "" ";{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Components Name "" "" "" "" -Study Protocol Components Type "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 88778d00..00000000 --- a/cubi_tk/isa_tpl/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,7 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set source_meta = cookiecutter.source_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -Source Name Characteristics[Organism] Term Source REF Term Accession Number{%+ for meta in source_meta %} Characteristics[{{meta}}]{% endfor %} Protocol REF Parameter Value[Method] Performer Date Sample Name{%+ for meta in sample_meta %} Characteristics[{{meta}}]{% endfor %} -{% for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606{%+ for meta in source_meta %} {% endfor %} Sample collection {{sample_name|replace("-", "_")}}{%+ for meta in sample_meta %} {% endfor %} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json deleted file mode 100644 index bb0e6d9d..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core/cookiecutter.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "sample1,sample2", - "a_measurement_type": "transcription profiling", - "source_type": ["hiPSC", "tissue"], - "source_meta": "Genetic modfications,Passage", - "model_type": ["3D", "2D"], - "sample_meta": "Tissue type,Differentiation duration,Condition,Treatment,Treatment duration", - "library_type": ["Single-Cell", "Bulk"], - "library_kit": "{{'SC3Pv3' if cookiecutter.library_type == 'Single-Cell' else ''}}", - "dissociation_meta": "{{'Cell count,Removal debris,Removal dead cell,Removal ab cell,Cell fixation,Cell viability' if cookiecutter.library_type == 'Single-Cell' else 'Cell count'}}", - "library_construction_meta": "{{'Sequencing kit,RNA amount,QC cell load recovery,QC tape fragment size' if cookiecutter.library_type == 'Single-Cell' else 'Sequencing kit,RNA amount,QC tape fragment size'}}", - "sequencing_meta": "Platform,Instrument model,No. targeted reads,QC-notes", - "study_title": "{{cookiecutter.investigation_title}}", - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "nucleotide sequencing", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index 46585a8e..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,8 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Sample Name Protocol REF Parameter Value[Passed] Protocol REF Parameter Value[Dissociation method]{%+ for meta in dissociation_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Library kit] Parameter Value[Library type] Parameter Value[Multiplex genotype] Parameter Value[Multiplex sample] Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Extract Name Protocol REF Parameter Value[Sequencing run] Parameter Value[Library prefix] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name -{% for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} OverallQC Dissociation {%+ for meta in dissociation_meta %} {% endfor %} Library construction {{cookiecutter.library_kit}} {{cookiecutter.library_type}} Gene Expression {%+ for meta in library_construction_meta %} {% endfor %} {{sample_name}}_GEX Nucleic acid sequencing {{sample_name}}_GEX {%+ for meta in sequencing_meta %} {% endfor %} {{sample_name}} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index f2a03e58..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,100 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_stem_cell_core -Comment[Last Opened With Configuration] bih_stem_cell_core -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -{% set source_meta = cookiecutter.source_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Study Protocol Name OverallQC Differentiation Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type OverallQC Differentiation Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type Term Accession Number "" "" "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" "" "" -Study Protocol Description "" "" "" "" "" "" -Study Protocol URI "" "" "" "" "" "" -Study Protocol Version "" "" "" "" "" "" -Study Protocol Parameters Name Passed Protocol numbers;Culture type;Differentiation dates;No. of passages;Well format SampleType;Collection reagent Dissociation method{% for meta in dissociation_meta -%};{{meta}}{% endfor %} Library kit;Library type;Multiplex genotype;Multiplex sample;Multiplex oligo{% for meta in library_construction_meta -%};{{meta}}{% endfor %} Sequencing run;Library prefix;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %} -Study Protocol Parameters Name Term Accession Number "" ";;;;" ";" "{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Parameters Name Term Source REF "" ";;;;" ";" "{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Components Name "" "" "" "" "" "" -Study Protocol Components Type "" "" "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 7df99bbb..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,7 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set source_meta = cookiecutter.source_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[ExperimentName] Characteristics[Source Type] Characteristics[Cellline]{%+ for meta in source_meta %} Characteristics[{{meta}}]{% endfor %} Protocol REF Parameter Value[Protocol numbers] Parameter Value[Culture type] Parameter Value[Differentiation dates] Parameter Value[No. of passages] Parameter Value[Well format] Performer Protocol REF Parameter Value[SampleType] Parameter Value[Collection reagent] Performer Date Sample Name{%+ for meta in sample_meta %} Characteristics[{{meta}}]{% endfor %} -{% for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 {{cookiecutter.source_type}} BIHi00XYZ{%+ for meta in source_meta %} {% endfor %} Differentiation {{cookiecutter.model_type}} Sample collection {{sample_name|replace("-", "_")}}{%+ for meta in sample_meta %} {% endfor %} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json deleted file mode 100644 index d11b52c0..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/cookiecutter.json +++ /dev/null @@ -1,20 +0,0 @@ -{ - "group": "CoreRnD", - "study_title": "Study Title", - "sample_numbers": "0001,0002", - "investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", - "source_type": ["hiPSC", "tissue"], - "cellline": "", - "cellculture_meta": "Expansion ID,Media,Matrix", - "model_type": ["2D", "3D"], - "sample_meta": "Experiment Name,Experiment Identifier,Tissue type,Differentiation duration,Condition,Treatment,Treatment duration", - "a_measurement_type": "transcription profiling", - "a_technology_type": "nucleotide sequencing", - "library_kit": "mRNA", - "library_construction_meta": "Library selection,Target insert size", - "sequencing_meta": "Platform,Instrument model,No. targeted reads,Paired-End", - "s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", - "assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", - "assay_name": "GEX_{{cookiecutter.a_measurement_type|replace(' ', '_')}}", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index b0eec56e..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,7 +0,0 @@ -{% set sample_numbers = cookiecutter.sample_numbers.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Sample Name Protocol REF Parameter Value[Passed] Protocol REF Parameter Value[Extraction kit] Parameter Value[RNA amount (ng)] Parameter Value[Tapestation QC RIN] Performer Date Extract Name Protocol REF Parameter Value[Library kit] Parameter Value[Library type]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Sequencing run] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name -{% for sample_no in sample_numbers -%} -GEX-BLK_{{sample_no}} OverallQC RNA extraction GEX-BLK_{{sample_no}} Library construction {{cookiecutter.library_kit}} Gene expression {%+ for meta in library_construction_meta %} {% endfor %} Nucleic acid sequencing {%+ for meta in sequencing_meta %} {% endfor %} GEX-BLK_{{sample_no}} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 7c5dc373..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,99 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] bih_cancer -Comment[Last Opened With Configuration] bih_cancer -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Study Protocol Name OverallQC Cell culture Differentiation Sample collection RNA extraction Library construction Nucleic acid sequencing -Study Protocol Type OverallQC Cell culture Differentiation Sample collection RNA extraction Library construction Nucleic acid sequencing -Study Protocol Type Term Accession Number "" "" "" "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" "" "" "" -Study Protocol Description "" "" "" "" "" "" "" -Study Protocol URI "" "" "" "" "" "" "" -Study Protocol Version "" "" "" "" "" "" "" -Study Protocol Parameters Name Passed Passage{% for meta in cellculture_meta %};{{meta}}{% endfor %} Protocol numbers;Culture type;Differentiation dates;No. of passages;Well format;Day SampleType;Collection reagent Extraction kit;RNA amount (ng);Tapestation QC RIN Library kit;Library type{% for meta in library_construction_meta -%};{{meta}}{% endfor %} Sequencing run;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %} -Study Protocol Parameters Name Term Accession Number "" "{% for meta in cellculture_meta %};{% endfor %}" ";;;;;" ";" ";;" ";{% for meta in library_construction_meta -%};{% endfor %}" ";;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Parameters Name Term Source REF "" "{% for meta in cellculture_meta %};{% endfor %}" ";;;;;" ";" ";;" ";{% for meta in library_construction_meta -%};{% endfor %}" ";;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Components Name "" "" "" "" "" "" "" -Study Protocol Components Type "" "" "" "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 0f25b5ba..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_bulk/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,7 +0,0 @@ -{% set sample_numbers = cookiecutter.sample_numbers.split(",") -%} -{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Source Type] Characteristics[Cellline] Characteristics[Genetic modfications] Protocol REF Parameter Value[Passage]{%+ for meta in cellculture_meta %} Parameter Value[{{meta}}]{% endfor %} Protocol REF Parameter Value[Protocol numbers] Parameter Value[Culture type] Parameter Value[Differentiation dates] Parameter Value[No. of passages] Parameter Value[Well format] Parameter Value[Day] Performer Protocol REF Parameter Value[SampleType] Parameter Value[Collection reagent] Performer Date Sample Name{%+ for meta in sample_meta %} Characteristics[{{meta}}]{% endfor %} -{% for sample_no in sample_numbers -%} -{{cookiecutter.cellline}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 {{cookiecutter.source_type}} {{cookiecutter.cellline}} Cell culture {%+ for meta in cellculture_meta %} {% endfor %} Differentiation {{cookiecutter.model_type}} Sample collection GEX-BLK_{{sample_no}}{%+ for meta in sample_meta %} {% endfor %} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json b/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json deleted file mode 100644 index 31f2d0eb..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/cookiecutter.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "group": "CoreRnD", - "study_title": "Study Title", - "sample_names": "sample1,sample2", - "investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", - "source_type": ["hiPSC", "tissue"], - "cellline": "", - "cellculture_meta": "Expansion ID,Media,Matrix", - "model_type": ["3D", "2D"], - "sample_meta": "Experiment Name,Experiment Identifier,Tissue type,Differentiation duration,Condition,Treatment,Treatment duration", - "a_measurement_type": "transcription profiling", - "a_technology_type": "nucleotide sequencing", - "library_kit": [ - "SC3Pv3", - "SC3Pv2", - "SC5P-PE", - "SC5P-R2", - "threeprime", - "fiveprime" - ], - "dissociation_meta": "Cell count,Removal debris,Removal dead cell,Cell fixation,Cell viability,No. cells used", - "library_construction_meta": "RNA amount,QC cell load recovery,QC tape fragment size,Library concentration (ng/µl)", - "sequencing_meta": "Platform,Instrument model,No. targeted reads", - "_library_types": { - "GEX": {"full" : "Gene Expression", "short": "GEX"}, - "antibody": {"full" : "Antibody Capture", "short": "surface"}, - "VDJ": {"full" : "VDJ-T", "short": "TCR"}, - "other": {"full" : "other", "short": "XXX"}, - "another": {"full" : "foobar", "short": "YYY"}, - "CellPlex": {"full": "Multiplexing Capture", "short": "MPX"} - }, - "library_type": ["GEX", "GEX+antibody", "GEX+VDJ", "GEX+other", "GEX+antibody+VDJ", "GEX+other+another"], - "sample_multiplexing": ["No", "CellPlex", "TotalSeq", "Other"], - "genotype_multiplexing": ["no", "yes"], - "s_file_name": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", - "assay_prefix": "{{cookiecutter.study_title|replace(' ', '_')|replace('/', '-')}}", - "assay_name": "{{cookiecutter.library_type}}_{{cookiecutter.a_measurement_type|replace(' ', '_')}}", - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index c0628f41..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,15 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set features = cookiecutter.library_type.split("+") -%} -{% if cookiecutter.sample_multiplexing == "CellPlex" -%}{{ features.append("CellPlex") or "" }}{% endif -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Sample Name Protocol REF Parameter Value[Passed] Protocol REF Parameter Value[Dissociation method]{%+ for meta in dissociation_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Protocol REF Parameter Value[Library kit] Parameter Value[Library type] Parameter Value[Multiplex genotype] Parameter Value[Multiplex sample] Parameter Value[Multiplex oligo]{%+ for meta in library_construction_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Extract Name Protocol REF Parameter Value[Sequencing batch] Parameter Value[Fastq prefix] Parameter Value[Barcode kit] Parameter Value[Barcode name]{%+ for meta in sequencing_meta %} Parameter Value[{{meta}}]{% endfor %} Performer Date Library Name -{% for sample_name in sample_names -%} -{% for f_name in features -%} -{% set feature = cookiecutter._library_types[f_name].full -%} -{% set abr = cookiecutter._library_types[f_name].short -%} -{% set sample = sample_name|replace(" ", "_") -%} -{{sample}} OverallQC Dissociation {%+ for meta in dissociation_meta %} {% endfor %} Library construction {{cookiecutter.library_kit}} {{feature}} {{cookiecutter.genotype_multiplexing == 'yes'}} {{cookiecutter.sample_multiplexing}} {%+ for meta in library_construction_meta %} {% endfor %} {{sample}}_{{abr}} Nucleic acid sequencing {{sample}}_{{abr}} {%+ for meta in sequencing_meta %} {% endfor %} {{sample}} -{% endfor -%} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index a3e16e05..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,100 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] bih_cancer -Comment[Last Opened With Configuration] bih_cancer -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt -Study Assay Measurement Type {{cookiecutter.a_measurement_type}} -Study Assay Measurement Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000424 -Study Assay Measurement Type Term Source REF OBI -Study Assay Technology Type {{cookiecutter.a_technology_type}} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626 -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -{% set dissociation_meta = cookiecutter.dissociation_meta.split(",") -%} -{% set library_construction_meta = cookiecutter.library_construction_meta.split(",") -%} -{% set sequencing_meta = cookiecutter.sequencing_meta.split(",") -%} -Study Protocol Name OverallQC Cell culture Differentiation Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type OverallQC Cell culture Differentiation Sample collection Dissociation Library construction Nucleic acid sequencing -Study Protocol Type Term Accession Number "" "" "" "" "" "" "" -Study Protocol Type Term Source REF "" "" "" "" "" "" "" -Study Protocol Description "" "" "" "" "" "" "" -Study Protocol URI "" "" "" "" "" "" "" -Study Protocol Version "" "" "" "" "" "" "" -Study Protocol Parameters Name Passed Passage{% for meta in cellculture_meta -%};{{meta}}{% endfor %} Protocol numbers;Culture type;Differentiation dates;No. of passages;Well format;Day Sample type;Collection reagent Dissociation method{% for meta in dissociation_meta -%};{{meta}}{% endfor %} Library kit;Library type;Multiplex genotype;Multiplex sample;Multiplex oligo{% for meta in library_construction_meta -%};{{meta}}{% endfor %} Sequencing batch;Fastq prefix;Barcode kit;Barcode name{% for meta in sequencing_meta -%};{{meta}}{% endfor %} -Study Protocol Parameters Name Term Accession Number "" "{% for meta in cellculture_meta -%};{% endfor %}" ";;;;;" ";" "{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Parameters Name Term Source REF "" "{% for meta in cellculture_meta -%};{% endfor %}" ";;;;;" ";" "{% for meta in dissociation_meta -%};{% endfor %}" ";;;;{% for meta in library_construction_meta -%};{% endfor %}" ";;;{% for meta in sequencing_meta -%};{% endfor %}" -Study Protocol Components Name "" "" "" "" "" "" "" -Study Protocol Components Type "" "" "" "" "" "" "" -Study Protocol Components Type Term Accession Number "" "" "" "" "" "" "" -Study Protocol Components Type Term Source REF "" "" "" "" "" "" "" -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 8eaa7816..00000000 --- a/cubi_tk/isa_tpl/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,8 +0,0 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{% set cellculture_meta = cookiecutter.cellculture_meta.split(",") -%} -{% set sample_meta = cookiecutter.sample_meta.split(",") -%} -Source Name Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Source Type] Characteristics[Cellline] Characteristics[Genetic modifications] Protocol REF Parameter Value[Passage]{%+ for meta in cellculture_meta %} Parameter Value[{{meta}}]{% endfor %} Protocol REF Parameter Value[Protocol numbers] Parameter Value[Culture type] Parameter Value[Differentiation dates] Parameter Value[No. of passages] Parameter Value[Well format] Parameter Value[Day] Performer Protocol REF Parameter Value[Sample type] Parameter Value[Collection reagent] Performer Date Sample Name{%+ for meta in sample_meta %} Characteristics[{{meta}}]{% endfor %} -{% for sample_name in sample_names -%} -{% set sample = sample_name|replace(" ", "_") -%} -{{cookiecutter.cellline}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 {{cookiecutter.source_type}} {{cookiecutter.cellline}} Cell culture {%+ for meta in cellculture_meta %} {% endfor %} Differentiation {{cookiecutter.model_type}} Sample collection {{sample}}{%+ for meta in sample_meta %} {% endfor %} -{% endfor -%} diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/cookiecutter.json b/cubi_tk/isa_tpl/isatab-tumor_normal_dna/cookiecutter.json deleted file mode 120000 index a59952b6..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/cookiecutter.json +++ /dev/null @@ -1 +0,0 @@ -../isatab-tumor_normal_triplets/cookiecutter.json \ No newline at end of file diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 120000 index 446adab2..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1 +0,0 @@ -../../isatab-tumor_normal_triplets/{{cookiecutter.i_dir_name}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt \ No newline at end of file diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 120000 index e3f2f70e..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1 +0,0 @@ -../../isatab-tumor_normal_triplets/{{cookiecutter.i_dir_name}}/i_Investigation.txt \ No newline at end of file diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 120000 index eadd3635..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_dna/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1 +0,0 @@ -../../isatab-tumor_normal_triplets/{{cookiecutter.i_dir_name}}/s_{{cookiecutter.s_file_name}}.txt \ No newline at end of file diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json deleted file mode 100644 index f69c36dd..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/cookiecutter.json +++ /dev/null @@ -1,72 +0,0 @@ -{ - "investigation_title": "Investigation Title", - "sample_names": "normal,tumor", - "a_measurement_type": [ - "exome sequencing", - "genome sequencing", - "panel sequencing" - ], - "lib_kit": [ - "Agilent SureSelect Human All Exon V6r2", - "Agilent SureSelect Human All Exon V5", - "Agilent SureSelect Human All Exon V4", - "Agilent SureSelect Human All Exon V7", - "IDT xGen Exome Research Panel V1.0", - "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "Illumina TruSeq PCR-free", - "Illumina TruSeq Nano" - ], - "lib_kits": { - "Agilent SureSelect Human All Exon V6r2": { - "name": "Agilent SureSelect Human All Exon V6r2", - "cat_id": "S04380110" - }, - "Agilent SureSelect Human All Exon V5": { - "name": "Agilent SureSelect Human All Exon V5", - "cat_id": "S04380110" - }, - "Agilent SureSelect Human All Exon V4": { - "name": "Agilent SureSelect Human All Exon V4", - "cat_id": "S03723314" - }, - "Agilent SureSelect Human All Exon V7": { - "name": "Agilent SureSelect Human All Exon V7", - "cat_id": "S31285117" - }, - "IDT xGen Exome Research Panel V1.0": { - "name": "IDT xGen Exome Research Panel V1.0", - "cat_id": "" - }, - "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in": { - "name": "IDT xGen Exome Research Panel V1.0 with YCGA 620kbp spike-in", - "cat_id": "" - }, - "Illumina TruSeq PCR-free": { - "name": "Illumina TruSeq PCR-free", - "cat_id": "" - }, - "Illumina TruSeq Nano": { - "name": "Illumina TruSeq Nano", - "cat_id": "" - } - }, - "instrument": "Illumina NextSeq 500", - "center_name": "", - "center_contact": "", - - "study_title": "{{cookiecutter.investigation_title}}", - "is_triplet": null, - "s_file_name": "{{cookiecutter.investigation_title|replace(' ', '_')}}", - "assay_prefix": "{{cookiecutter.s_file_name|lower}}", - "a_technology_type": "nucleotide sequencing", - "a_measurement_abbreviation": "{% if cookiecutter.a_measurement_type == 'exome sequencing' %}WES{% else %}WGS{% endif %}", - "assay_name": "{{cookiecutter.a_measurement_type|replace(' ', '_')}}_{{cookiecutter.a_technology_type|replace(' ', '_')}}", - "sample_type": "x-generic-remote", - "lib_strategy": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}WXS{% else %}WGS{% endif %}", - "lib_selection": "{% if cookiecutter.a_measurement_abbreviation == 'WES' %}Hybrid Selection{% else %}RANDOM{% endif %}", - "lib_layout": [ - "PAIRED", - "SINGLE" - ], - "__output_dir": "Required variable. Do not remove." -} diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt deleted file mode 100644 index 7e13e828..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Parameter Value[Library strand specificity] Comment[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Library Name Characteristics[Folder name] Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 2)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date Raw Data File -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Nucleic acid extraction RNA-Seq {{sample_name|replace("-", "_")}}-N1-RNA1 Library construction RNA-Seq TRANSCRIPTOMIC RNA-Seq PolyA PAIRED Illumina TruSeq Stranded mRNA REVERSE {{sample_name|replace("-", "_")}}-N1-RNA1-RNA-Seq1 {{sample_name}} Nucleic acid sequencing RNA-Seq ILLUMINA Illumina HiSeq 4000 Phred+33 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt deleted file mode 100644 index 1e93d2bc..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Sample Name Protocol REF Parameter Value[Concentration measurement] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Provider name] Parameter Value[Provider contact] Parameter Value[Provider project ID] Parameter Value[Provider sample ID] Parameter Value[Provider QC status] Parameter Value[Requestor contact] Parameter Value[Requestor project] Parameter Value[Requestor sample ID] Parameter Value[Concentration measurement] Parameter Value[Library source] Parameter Value[Library strategy] Parameter Value[Library selection] Parameter Value[Library layout] Parameter Value[Library kit] Parameter Value[Library kit catalogue ID] Parameter Value[Target insert size] Parameter Value[Wet-lab insert size] Parameter Value[Barcode kit] Parameter Value[Barcode kit catalogue ID] Parameter Value[Barcode name] Parameter Value[Barcode sequence] Performer Date Library Name Characteristics[Folder Name] Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Platform] Parameter Value[Instrument model] Parameter Value[Target read length] Parameter Value[Target read length (mate 2)] Parameter Value[Base quality encoding] Parameter Value[Center name] Parameter Value[Center contact] Performer Date Raw Data File -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{sample_name|replace("-", "_")}}-N1-DNA1 Library construction {{cookiecutter.a_measurement_abbreviation}} GENOMIC {{cookiecutter.lib_strategy}} {{cookiecutter.lib_selection}} {{cookiecutter.lib_layout}} {{cookiecutter.lib_kits[cookiecutter.lib_kit].name}} {{cookiecutter.lib_kits[cookiecutter.lib_kit].cat_id}} {{sample_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{sample_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 -{% endfor %} diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/i_Investigation.txt deleted file mode 100644 index 9c925519..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO -Term Source Version 48 35 10 12 570 2.8 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title {{cookiecutter.investigation_title}} -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_cancer -Comment[Last Opened With Configuration] bih_cancer -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier {{cookiecutter.s_file_name}} -Study Title {{cookiecutter.investigation_title}} -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_{{cookiecutter.s_file_name}}.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt{% if cookiecutter.is_triplet == True %} a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt{% endif %} -Study Assay Measurement Type {{cookiecutter.a_measurement_type}}{% if cookiecutter.is_triplet == True %} transcriptome profiling{% endif %} -Study Assay Measurement Type Term Accession Number ""{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000424{% endif %} -Study Assay Measurement Type Term Source REF ""{% if cookiecutter.is_triplet == True %} ""{% endif %} -Study Assay Technology Type {{cookiecutter.a_technology_type}}{% if cookiecutter.is_triplet == True %} nucleotide sequencing{% endif %} -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000626{% if cookiecutter.is_triplet == True %} http://purl.obolibrary.org/obo/OBI_0000626{% endif %} -Study Assay Technology Type Term Source REF OBI -Study Assay Technology Platform Illumina -STUDY PROTOCOLS -Study Protocol Name Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}{% if cookiecutter.is_triplet == True %} Nucleic acid extraction RNA-Seq Library construction RNA-Seq Nucleic acid sequencing RNA-Seq{% endif %} -Study Protocol Type Sample collection Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} Library construction {{cookiecutter.a_measurement_abbreviation}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}}{% if cookiecutter.is_triplet == True %} Nucleic acid extraction RNA-Seq Library construction RNA-Seq Nucleic acid sequencing RNA-Seq{% endif %} -Study Protocol Type Term Accession Number "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Type Term Source REF "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Description "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol URI "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Version "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Parameters Name "" Concentration measurement "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Barcode name;Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Instrument model;Center name"{% if cookiecutter.is_triplet == True %} "Concentration measurement" "Provider project ID;Library source;Library selection;Library layout;Barcode sequence;Wet-lab insert size;Requestor contact;Library kit;Barcode name;Provider contact;Concentration measurement;Provider sample ID;Target insert size;Provider name;Requestor project;Requestor sample ID;Barcode kit;Barcode kit catalogue ID;Provider QC status;Library strategy" "Base quality encoding;Platform;Center contact;Target read length;Target read length (mate 2);Instrument model;Center name"{% endif %} -Study Protocol Parameters Name Term Accession Number "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;"{% if cookiecutter.is_triplet == True %} "" ";;;;;;;;;;;;;;;;;;;" ";;;;;;"{% endif %} -Study Protocol Parameters Name Term Source REF "" "" ";;;;;;;;;;;;;;;;;;;" ";;;;"{% if cookiecutter.is_triplet == True %} "" ";;;;;;;;;;;;;;;;;;;" ";;;;;;"{% endif %} -Study Protocol Components Name "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Components Type "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Components Type Term Accession Number "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -Study Protocol Components Type Term Source REF "" "" "" ""{% if cookiecutter.is_triplet == True %} "" "" ""{% endif %} -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt deleted file mode 100644 index 49431b97..00000000 --- a/cubi_tk/isa_tpl/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ /dev/null @@ -1,5 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[External links] Characteristics[Source type] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[ICD10 code] Term Source REF Term Accession Number Characteristics[cBioPortal ethnicity] Characteristics[Population super code] Characteristics[Population code] Characteristics[Strain] Term Source REF Term Accession Number Characteristics[Germline] Characteristics[Consent DUO Terms] Term Source REF Term Accession Number Characteristics[Consent reuse time limit] Characteristics[Consent reuse in diseases] Term Source REF Term Accession Number Characteristics[Consent retraction date] Characteristics[Consent retraction note] Characteristics[ODM visibility mode] Characteristics[ODM visibility fields] Characteristics[Age at sampling] Unit Term Source REF Term Accession Number Characteristics[Age at diagnosis] Unit Term Source REF Term Accession Number Protocol REF Performer Date Sample Name Characteristics[External links] Characteristics[Tissue type] Characteristics[Tissue quantity] Unit Term Source REF Term Accession Number Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number Characteristics[Is tumor] Characteristics[Is Metastasis] Term Source REF Term Accession Number Characteristics[TNM stage] Characteristics[OncoTree cancer type] Term Source REF Term Accession Number Characteristics[Tumor grade] -{% set sample_names = cookiecutter.sample_names.split(",") -%} -{%- for sample_name in sample_names -%} -{{sample_name|replace("-", "_")}} {{cookiecutter.sample_type}}:{{sample_name}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 none Sample collection {{sample_name|replace("-", "_")}}-N1 Y/N True/False -{% endfor %} diff --git a/requirements/base.txt b/requirements/base.txt index f4badf7c..bf569733 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -66,3 +66,6 @@ sodar-cli ==0.1.0 # Python iRODS client python-irodsclient==1.1.3 + +# CUBI ISA-Tab Templates +-e git+https://github.com/bihealth/cubi-isa-templates.git@13ec5a83c9f7871d64064bbae658a0009d4bf113#egg=cubi-isa-templates diff --git a/setup.py b/setup.py index 2a244a04..6d45163e 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ def parse_requirements(path): fname = line.split()[1] inner_path = os.path.join(os.path.dirname(path), fname) requirements += parse_requirements(inner_path) - elif line != "" and not line.startswith("#"): + elif line != "" and not line.startswith("#") and not line.startswith("-e"): requirements.append(line) return requirements @@ -49,6 +49,10 @@ def parse_requirements(path): entry_points={"console_scripts": ("cubi-tk = cubi_tk.__main__:main",)}, description="Tooling for connecting GitLab, pipelines, and SODAR at CUBI.", install_requires=install_requirements, + dependency_links=[ + "git+https://github.com/bihealth/cubi-isa-templates.git@" + "13ec5a83c9f7871d64064bbae658a0009d4bf113#egg=cubi-isa-templates" + ], license="MIT license", long_description=readme + "\n\n" + changelog, long_description_content_type="text/markdown", From 8f4d8342f7bceebb64fe86bf9718e6416adc31fc Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 11:47:17 +0200 Subject: [PATCH 02/14] refactor: Use published version 0.1.0 of cubi-isa-templates --- requirements/base.txt | 5 +++-- setup.py | 4 ---- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/requirements/base.txt b/requirements/base.txt index bf569733..bafbe6b4 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -4,8 +4,9 @@ attrs cattrs -# Cookiecutter for templating ISA-tab directories. -cookiecutter >=1.7.3 +# For ISA-tab templates. +cookiecutter==2.3.0 +cubi-isa-templates==0.1.0 # Easy logging. logzero diff --git a/setup.py b/setup.py index 6d45163e..2e6aeec0 100644 --- a/setup.py +++ b/setup.py @@ -49,10 +49,6 @@ def parse_requirements(path): entry_points={"console_scripts": ("cubi-tk = cubi_tk.__main__:main",)}, description="Tooling for connecting GitLab, pipelines, and SODAR at CUBI.", install_requires=install_requirements, - dependency_links=[ - "git+https://github.com/bihealth/cubi-isa-templates.git@" - "13ec5a83c9f7871d64064bbae658a0009d4bf113#egg=cubi-isa-templates" - ], license="MIT license", long_description=readme + "\n\n" + changelog, long_description_content_type="text/markdown", From 6fc16145a36b2e5f82c4f1ff87ed8bfad36dbe7e Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 11:49:09 +0200 Subject: [PATCH 03/14] remove no longer used config logic --- cubi_tk/isa_tpl/__init__.py | 4 ---- 1 file changed, 4 deletions(-) diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py index 44ae7eff..a12d1111 100644 --- a/cubi_tk/isa_tpl/__init__.py +++ b/cubi_tk/isa_tpl/__init__.py @@ -62,10 +62,6 @@ def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False): output_base = os.path.dirname(output_dir) extra_context["__output_dir"] = os.path.basename(output_dir) - # FIXME: better solution? (added because args.var_is_triplet is None) - if "is_triplet" in tpl.configuration: - extra_context["is_triplet"] = tpl.configuration["is_triplet"] - logger.info("Start running cookiecutter") logger.info(" template path: %s", tpl.path) logger.info(" vars from CLI: %s", extra_context) From 884651c43c364505339322bb2d3096279226993e Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 11:54:18 +0200 Subject: [PATCH 04/14] make isa-tpl command less verbose by default --- cubi_tk/isa_tpl/__init__.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py index a12d1111..7ab30c35 100644 --- a/cubi_tk/isa_tpl/__init__.py +++ b/cubi_tk/isa_tpl/__init__.py @@ -55,8 +55,9 @@ def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False): if getattr(args, "var_%s" % name, None) is not None: extra_context[name] = getattr(args, "var_%s" % name) - logger.info(tpl.configuration) - logger.info(args) + if args.verbose: + logger.info(tpl.configuration) + logger.info(args) output_dir = os.path.realpath(args.output_dir) output_base = os.path.dirname(output_dir) From 24c370c6b12faabda6447ccfc03aa6451f230e43 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 12:55:30 +0200 Subject: [PATCH 05/14] remove os module import --- cubi_tk/isa_tpl/__init__.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py index 7ab30c35..fffd4420 100644 --- a/cubi_tk/isa_tpl/__init__.py +++ b/cubi_tk/isa_tpl/__init__.py @@ -36,7 +36,6 @@ import argparse from functools import partial -import os from pathlib import Path from cookiecutter.main import cookiecutter @@ -59,9 +58,9 @@ def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False): logger.info(tpl.configuration) logger.info(args) - output_dir = os.path.realpath(args.output_dir) - output_base = os.path.dirname(output_dir) - extra_context["__output_dir"] = os.path.basename(output_dir) + output_dir = Path(args.output_dir).resolve() + output_base = Path(output_dir).parent + extra_context["__output_dir"] = Path(output_dir).name logger.info("Start running cookiecutter") logger.info(" template path: %s", tpl.path) From 4ca48b90107972e361861b64ce4fd5587d0ee283 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 13:13:56 +0200 Subject: [PATCH 06/14] remove double dependency --- requirements/base.txt | 3 --- 1 file changed, 3 deletions(-) diff --git a/requirements/base.txt b/requirements/base.txt index bafbe6b4..f416e473 100644 --- a/requirements/base.txt +++ b/requirements/base.txt @@ -67,6 +67,3 @@ sodar-cli ==0.1.0 # Python iRODS client python-irodsclient==1.1.3 - -# CUBI ISA-Tab Templates --e git+https://github.com/bihealth/cubi-isa-templates.git@13ec5a83c9f7871d64064bbae658a0009d4bf113#egg=cubi-isa-templates From 91d139388b01b69734472b6425c1ebae322c495e Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 13:18:03 +0200 Subject: [PATCH 07/14] fix tests --- tests/test_isa_tpl.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index 0c769ea4..6f344812 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -39,9 +39,9 @@ def test_run_cookiecutter_isatab_germline(tmp_path): assert output_path.exists() assert (output_path / "i_Investigation.txt").exists() assert ( - output_path / "a_investigation_title_exome_sequencing_nucleotide_sequencing.txt" + output_path / "a_investigation_title_exome_sequencing.txt" ).exists() - assert (output_path / "s_Investigation_Title.txt").exists() + assert (output_path / "s_investigation_title.txt").exists() def test_run_cookiecutter_isatab_ms_meta_biocrates(tmp_path): From b60990d0cb3fa63a2131ccfd2252e8acf3bd3b26 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 13:19:19 +0200 Subject: [PATCH 08/14] make CI happy --- cubi_tk/archive/readme.py | 1 - tests/test_isa_tpl.py | 4 +--- 2 files changed, 1 insertion(+), 4 deletions(-) diff --git a/cubi_tk/archive/readme.py b/cubi_tk/archive/readme.py index 976f2a17..2be38c93 100644 --- a/cubi_tk/archive/readme.py +++ b/cubi_tk/archive/readme.py @@ -18,7 +18,6 @@ from . import common from ..common import execute_shell_commands - _TEMPLATE_DIR = os.path.join(os.path.dirname(__file__), "templates") TEMPLATE = IsaTabTemplate( diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index 6f344812..9602683b 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -38,9 +38,7 @@ def test_run_cookiecutter_isatab_germline(tmp_path): assert output_path.exists() assert (output_path / "i_Investigation.txt").exists() - assert ( - output_path / "a_investigation_title_exome_sequencing.txt" - ).exists() + assert (output_path / "a_investigation_title_exome_sequencing.txt").exists() assert (output_path / "s_investigation_title.txt").exists() From a7a1471c091f9016aef99b03e14229b5260c5d65 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 13:24:16 +0200 Subject: [PATCH 09/14] remove temp hack for editable modules --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 2e6aeec0..2a244a04 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ def parse_requirements(path): fname = line.split()[1] inner_path = os.path.join(os.path.dirname(path), fname) requirements += parse_requirements(inner_path) - elif line != "" and not line.startswith("#") and not line.startswith("-e"): + elif line != "" and not line.startswith("#"): requirements.append(line) return requirements From de23383d50159a9eb43c4ecc794cdfc64ce8ffe6 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 13:30:17 +0200 Subject: [PATCH 10/14] remove double invokation of Path --- cubi_tk/isa_tpl/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cubi_tk/isa_tpl/__init__.py b/cubi_tk/isa_tpl/__init__.py index fffd4420..8a894895 100644 --- a/cubi_tk/isa_tpl/__init__.py +++ b/cubi_tk/isa_tpl/__init__.py @@ -59,7 +59,7 @@ def run_cookiecutter(tpl, args, _parser=None, _subparser=None, no_input=False): logger.info(args) output_dir = Path(args.output_dir).resolve() - output_base = Path(output_dir).parent + output_base = output_dir.parent extra_context["__output_dir"] = Path(output_dir).name logger.info("Start running cookiecutter") From 1a47353493b0d4d0ebb8e6935095c44aa2dbafb9 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 14:32:50 +0200 Subject: [PATCH 11/14] remove template tests; add unittest for __init__ --- ..._title_Biocrates_MxP_Quant_500_Kit_FIA.txt | 6 -- ...n_title_Biocrates_MxP_Quant_500_Kit_LC.txt | 6 -- .../ms_meta_biocrates_01/i_Investigation.txt | 95 ------------------- .../s_investigation_title.txt | 6 -- tests/test_isa_tpl.py | 82 ++++------------ 5 files changed, 16 insertions(+), 179 deletions(-) delete mode 100644 tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt delete mode 100644 tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt delete mode 100644 tests/data/isa_tpl/ms_meta_biocrates_01/i_Investigation.txt delete mode 100644 tests/data/isa_tpl/ms_meta_biocrates_01/s_investigation_title.txt diff --git a/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt b/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt deleted file mode 100644 index 87acc7d2..00000000 --- a/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt +++ /dev/null @@ -1,6 +0,0 @@ -Sample Name Protocol REF Parameter Value[Post extraction] Parameter Value[Derivatization] Parameter Value[Phase] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Performer Date Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Term Source REF Term Accession Number Parameter Value[Ion source] Term Source REF Term Accession Number Parameter Value[Mass analyzer] Term Source REF Term Accession Number Parameter Value[Detector] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software name] Parameter Value[Aquisition software version] Parameter Value[Aquisition parameter] Performer Date MS Assay Name Raw Spectral Data File Comment[Batch] Comment[Well position] Comment[Sample type] Protocol REF Parameter Value[Analysis software name] Parameter Value[Analysis software version] Metabolite Assignment File Protocol REF Parameter Value[Software name] Parameter Value[Software version] Parameter Value[Report file] Performer Date -alpha-N1 Extraction B-LC alpha-N1-Meta1 Flow Injection Analysis B-FIA Mass spectrometry B-FIA QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 alpha-N1-Meta1-B-FIA1 Data transformation B-FIA Biocrates MetIDQ Quality Control B-FIA MeTaQuaC -beta-N1 Extraction B-LC beta-N1-Meta1 Flow Injection Analysis B-FIA Mass spectrometry B-FIA QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 beta-N1-Meta1-B-FIA1 Data transformation B-FIA Biocrates MetIDQ Quality Control B-FIA MeTaQuaC -gamma-N1 Extraction B-LC gamma-N1-Meta1 Flow Injection Analysis B-FIA Mass spectrometry B-FIA QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 gamma-N1-Meta1-B-FIA1 Data transformation B-FIA Biocrates MetIDQ Quality Control B-FIA MeTaQuaC - - diff --git a/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt b/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt deleted file mode 100644 index 446f345b..00000000 --- a/tests/data/isa_tpl/ms_meta_biocrates_01/a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt +++ /dev/null @@ -1,6 +0,0 @@ -Sample Name Protocol REF Parameter Value[Post extraction] Parameter Value[Derivatization] Parameter Value[Phase] Performer Date Extract Name Characteristics[Concentration] Unit Term Source REF Term Accession Number Protocol REF Parameter Value[Chromatography instrument] Term Source REF Term Accession Number Parameter Value[Column model] Term Source REF Term Accession Number Parameter Value[Column type] Term Source REF Term Accession Number Performer Date Protocol REF Parameter Value[Scan polarity] Parameter Value[Scan m/z range] Parameter Value[Instrument] Term Source REF Term Accession Number Parameter Value[Ion source] Term Source REF Term Accession Number Parameter Value[Mass analyzer] Term Source REF Term Accession Number Parameter Value[Detector] Term Source REF Term Accession Number Parameter Value[Aquisition mode] Term Source REF Term Accession Number Parameter Value[Aquisition software name] Parameter Value[Aquisition software version] Parameter Value[Aquisition parameter] Performer Date MS Assay Name Raw Spectral Data File Comment[Batch] Comment[Well position] Comment[Sample type] Protocol REF Parameter Value[Analysis software name] Parameter Value[Analysis software version] Metabolite Assignment File Protocol REF Parameter Value[Software name] Parameter Value[Software version] Parameter Value[Report file] Performer Date -alpha-N1 Extraction B-LC alpha-N1-Meta1 Chromatography B-LC Agilent UHPLC 1290 Mass spectrometry B-LC QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 alpha-N1-Meta1-B-LC1 Data transformation B-LC Biocrates MetIDQ Quality Control B-LC MeTaQuaC -beta-N1 Extraction B-LC beta-N1-Meta1 Chromatography B-LC Agilent UHPLC 1290 Mass spectrometry B-LC QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 beta-N1-Meta1-B-LC1 Data transformation B-LC Biocrates MetIDQ Quality Control B-LC MeTaQuaC -gamma-N1 Extraction B-LC gamma-N1-Meta1 Chromatography B-LC Agilent UHPLC 1290 Mass spectrometry B-LC QTRAP 5500 MS http://purl.obolibrary.org/obo/MS_1000931 gamma-N1-Meta1-B-LC1 Data transformation B-LC Biocrates MetIDQ Quality Control B-LC MeTaQuaC - - diff --git a/tests/data/isa_tpl/ms_meta_biocrates_01/i_Investigation.txt b/tests/data/isa_tpl/ms_meta_biocrates_01/i_Investigation.txt deleted file mode 100644 index 8ff2786c..00000000 --- a/tests/data/isa_tpl/ms_meta_biocrates_01/i_Investigation.txt +++ /dev/null @@ -1,95 +0,0 @@ -ONTOLOGY SOURCE REFERENCE -Term Source Name UO OBI NCBITAXON OMIM HP ORPHA CL MS -Term Source File http://data.bioontology.org/ontologies/UO http://data.bioontology.org/ontologies/OBI http://data.bioontology.org/ontologies/NCBITAXON http://data.bioontology.org/ontologies/OMIM http://data.bioontology.org/ontologies/HP http://data.bioontology.org/ontologies/ORDO http://data.bioontology.org/ontologies/CL http://data.bioontology.org/ontologies/MS -Term Source Version 48 35 10 12 570 2.8 2019-08-12 122 -Term Source Description Units of Measurement Ontology Ontology for Biomedical Investigations National Center for Biotechnology Information (NCBI) Organismal Classification Online Mendelian Inheritance in Man Human Phenotype Ontology Orphanet Rare Disease Ontology Cell Ontology Mass Spectrometry Ontology -INVESTIGATION -Investigation Identifier "" -Investigation Title Investigation Title -Investigation Description "" -Investigation Submission Date "" -Investigation Public Release Date "" -Comment[Created With Configuration] /path/to/isa-configurations/bih_studies/bih_ms_meta_biocrates -Comment[Last Opened With Configuration] bih_ms_meta_biocrates -INVESTIGATION PUBLICATIONS -Investigation PubMed ID -Investigation Publication DOI -Investigation Publication Author List -Investigation Publication Title -Investigation Publication Status -Investigation Publication Status Term Accession Number -Investigation Publication Status Term Source REF -INVESTIGATION CONTACTS -Investigation Person Last Name -Investigation Person First Name -Investigation Person Mid Initials -Investigation Person Email -Investigation Person Phone -Investigation Person Fax -Investigation Person Address -Investigation Person Affiliation -Investigation Person Roles -Investigation Person Roles Term Accession Number -Investigation Person Roles Term Source REF -STUDY -Study Identifier investigation_title -Study Title Investigation Title -Study Description "" -Comment[Study Grant Number] "" -Comment[Study Funding Agency] "" -Study Submission Date "" -Study Public Release Date "" -Study File Name s_investigation_title.txt -STUDY DESIGN DESCRIPTORS -Study Design Type -Study Design Type Term Accession Number -Study Design Type Term Source REF -STUDY PUBLICATIONS -Study PubMed ID -Study Publication DOI -Study Publication Author List -Study Publication Title -Study Publication Status -Study Publication Status Term Accession Number -Study Publication Status Term Source REF -STUDY FACTORS -Study Factor Name -Study Factor Type -Study Factor Type Term Accession Number -Study Factor Type Term Source REF -STUDY ASSAYS -Study Assay File Name a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt -Study Assay Measurement Type metabolite profiling metabolite profiling -Study Assay Measurement Type Term Accession Number "" "" -Study Assay Measurement Type Term Source REF "" "" -Study Assay Technology Type mass spectrometry mass spectrometry -Study Assay Technology Type Term Accession Number http://purl.obolibrary.org/obo/OBI_0000470 http://purl.obolibrary.org/obo/OBI_0000470 -Study Assay Technology Type Term Source REF OBI OBI -Study Assay Technology Platform Biocrates MxP Quant 500 Kit Biocrates MxP Quant 500 Kit -STUDY PROTOCOLS -Study Protocol Name Sample collection Extraction B-LC Labeling B-LC Chromatography B-LC Mass spectrometry B-LC Data transformation B-LC Quality Control B-LC Extraction B-FIA Labeling B-FIA Flow Injection Analysis B-FIA Mass spectrometry B-FIA Data transformation B-FIA Quality Control B-FIA -Study Protocol Type Sample collection Extraction B-LC Labeling B-LC Chromatography B-LC Mass spectrometry B-LC Data transformation B-LC Quality Control B-LC Extraction B-FIA Labeling B-FIA Flow Injection Analysis B-FIA Mass spectrometry B-FIA Data transformation B-FIA Quality Control B-FIA -Study Protocol Type Term Accession Number -Study Protocol Type Term Source REF -Study Protocol Description -Study Protocol URI -Study Protocol Version -Study Protocol Parameters Name Phase;Derivatization;Post extraction Column type;Chromatography instrument;Column model Scan polarity;Mass analyzer;Detector;Aquisition software name;Ion source;Aquisition mode;Instrument;Aquisition parameter;Aquisition software version;Scan m/z range Analysis software name;Analysis software version Report file;Software name;Software version Phase;Derivatization;Post extraction Scan polarity;Mass analyzer;Detector;Aquisition software name;Ion source;Aquisition mode;Instrument;Aquisition parameter;Aquisition software version;Scan m/z range Analysis software name;Analysis software version Report file;Software name;Software version -Study Protocol Parameters Name Term Accession Number ;; ;; ;;;;;;;;; ; ;; ;; ;;;;;;;;; ; ;; -Study Protocol Parameters Name Term Source REF ;; ;; ;;;;;;;;; ; ;; ;; ;;;;;;;;; ; ;; -Study Protocol Components Name -Study Protocol Components Type -Study Protocol Components Type Term Accession Number -Study Protocol Components Type Term Source REF -STUDY CONTACTS -Study Person Last Name -Study Person First Name -Study Person Mid Initials -Study Person Email -Study Person Phone -Study Person Fax -Study Person Address -Study Person Affiliation -Study Person Roles -Study Person Roles Term Accession Number -Study Person Roles Term Source REF diff --git a/tests/data/isa_tpl/ms_meta_biocrates_01/s_investigation_title.txt b/tests/data/isa_tpl/ms_meta_biocrates_01/s_investigation_title.txt deleted file mode 100644 index 92067314..00000000 --- a/tests/data/isa_tpl/ms_meta_biocrates_01/s_investigation_title.txt +++ /dev/null @@ -1,6 +0,0 @@ -Source Name Characteristics[UUID] Characteristics[Organism] Term Source REF Term Accession Number Characteristics[Sex] Characteristics[Disease type] Term Source REF Term Accession Number Characteristics[Disease status] Term Source REF Term Accession Number Characteristics[Age] Unit Term Source REF Term Accession Number Characteristics[BMI] Unit Term Source REF Term Accession Number Characteristics[HPO terms] Term Source REF Term Accession Number Comment[Disease notes] Protocol REF Performer Date Sample Name Characteristics[External links] Characteristics[Visit] Characteristics[Visit Centrum] Characteristics[Cell origin] Term Source REF Term Accession Number Characteristics[Cell type] Term Source REF Term Accession Number -alpha Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection alpha-N1 -beta Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection beta-N1 -gamma Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 UNKNOWN UNKNOWN UNKNOWN year UO http://purl.obolibrary.org/obo/UO_0000036 kilogram per square meter UO http://purl.obolibrary.org/obo/UO_0000086 Sample collection gamma-N1 - - diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index 9602683b..4f286452 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -4,69 +4,19 @@ output directory being created. """ -import filecmp -import glob -import os - -from cubi_tk.__main__ import setup_argparse -from cubi_tk.isa_tpl import TEMPLATES, run_cookiecutter - - -def test_run_cookiecutter_isatab_generic(tmp_path): - output_path = tmp_path / "output_dir" - parser, subparsers = setup_argparse() - args = parser.parse_args(["isa-tpl", "generic", str(output_path)]) - - run_isatab_generic = run_cookiecutter(TEMPLATES["generic"], no_input=True) - run_isatab_generic(args, parser, subparsers.choices[args.cmd]) - - assert output_path.exists() - assert (output_path / "i_Investigation.txt").exists() - assert ( - output_path / "a_investigation_title_transcription_profiling_nucleotide_sequencing.txt" - ).exists() - assert (output_path / "s_Investigation_Title.txt").exists() - - -def test_run_cookiecutter_isatab_germline(tmp_path): - output_path = tmp_path / "output_dir" - parser, subparsers = setup_argparse() - args = parser.parse_args(["isa-tpl", "germline", str(output_path)]) - - run_isatab_germline = run_cookiecutter(TEMPLATES["germline"], no_input=True) - run_isatab_germline(args, parser, subparsers.choices[args.cmd]) - - assert output_path.exists() - assert (output_path / "i_Investigation.txt").exists() - assert (output_path / "a_investigation_title_exome_sequencing.txt").exists() - assert (output_path / "s_investigation_title.txt").exists() - - -def test_run_cookiecutter_isatab_ms_meta_biocrates(tmp_path): - # Setup parameters - output_path = tmp_path / "output_dir" - parser, subparsers = setup_argparse() - args = parser.parse_args(["isa-tpl", "ms_meta_biocrates", str(output_path)]) - - # Create templates - run_isatpl = run_cookiecutter(TEMPLATES["ms_meta_biocrates"], no_input=True) - run_isatpl(args, parser, subparsers.choices[args.cmd]) - - # Check output files - assert output_path.exists() - assert (output_path / "i_Investigation.txt").exists() - assert (output_path / "a_investigation_title_Biocrates_MxP_Quant_500_Kit_FIA.txt").exists() - assert (output_path / "a_investigation_title_Biocrates_MxP_Quant_500_Kit_LC.txt").exists() - assert (output_path / "s_investigation_title.txt").exists() - - # Run altamisa validate here? I.e. it shouldn't throw exceptions or critical warnings. - - # Test against reference files - path_test = os.path.join(os.path.dirname(__file__), "data", "isa_tpl", "ms_meta_biocrates_01") - files = glob.glob(os.path.join(path_test, "*")) - match, mismatch, errors = filecmp.cmpfiles( - path_test, output_path, (os.path.basename(f) for f in files), shallow=False - ) - print([match, mismatch, errors]) - assert len(mismatch) == 0 - assert len(errors) == 0 +from argparse import ArgumentParser +from unittest.mock import patch + +from cubi_tk.isa_tpl.__init__ import validate_output_directory + + +@patch.object(ArgumentParser, "error") +def test_validate_output_directory(test_error, tmp_path): + parser = ArgumentParser() + d = tmp_path / "dir" + d.mkdir() + d2 = tmp_path / "no_dir" / "subdir" + validate_output_directory(parser, d) + validate_output_directory(parser, d2) + validate_output_directory(parser, d2.parent) + assert parser.error.call_count == 2 From ed604ee601c50023fa9b10499124ff5a6e2b0e84 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 14:37:50 +0200 Subject: [PATCH 12/14] remove obsolete docstring --- tests/test_isa_tpl.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index 4f286452..c9d5189f 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -1,8 +1,4 @@ -"""Tests for ``cubi_tk.isa_tpl``. - -We run cookiecutter for each template once for smoke-testing but don't actually validate the results behind the -output directory being created. -""" +"""Tests for ``cubi_tk.isa_tpl``.""" from argparse import ArgumentParser from unittest.mock import patch From 610f70b36720ab80ce5ba13f60173a7dbb9ce342 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 15:06:24 +0200 Subject: [PATCH 13/14] add run_cookiecutter smoketest --- tests/test_isa_tpl.py | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index c9d5189f..ad3cfa46 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -3,11 +3,22 @@ from argparse import ArgumentParser from unittest.mock import patch -from cubi_tk.isa_tpl.__init__ import validate_output_directory +from cubi_tk.isa_tpl.__init__ import run_cookiecutter, validate_output_directory +from cubi_isa_templates import TEMPLATES + + +def test_run_cookiecutter(tmp_path): + tpl = TEMPLATES["generic"] + args = type('test', (), {})() + path = tmp_path / "dir" + args.output_dir = str(path) + args.verbose = False + + run_cookiecutter(tpl, args, no_input = True) @patch.object(ArgumentParser, "error") -def test_validate_output_directory(test_error, tmp_path): +def test_validate_output_directory(mockerror, tmp_path): parser = ArgumentParser() d = tmp_path / "dir" d.mkdir() @@ -15,4 +26,4 @@ def test_validate_output_directory(test_error, tmp_path): validate_output_directory(parser, d) validate_output_directory(parser, d2) validate_output_directory(parser, d2.parent) - assert parser.error.call_count == 2 + assert mockerror.call_count == 2 From 76fa3cca956aec5d731e4a1657f1814452526659 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Mon, 18 Sep 2023 15:17:02 +0200 Subject: [PATCH 14/14] make CI happy --- tests/test_isa_tpl.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tests/test_isa_tpl.py b/tests/test_isa_tpl.py index ad3cfa46..b635d819 100644 --- a/tests/test_isa_tpl.py +++ b/tests/test_isa_tpl.py @@ -3,18 +3,19 @@ from argparse import ArgumentParser from unittest.mock import patch -from cubi_tk.isa_tpl.__init__ import run_cookiecutter, validate_output_directory from cubi_isa_templates import TEMPLATES +from cubi_tk.isa_tpl.__init__ import run_cookiecutter, validate_output_directory + def test_run_cookiecutter(tmp_path): tpl = TEMPLATES["generic"] - args = type('test', (), {})() + args = type("test", (), {})() path = tmp_path / "dir" args.output_dir = str(path) args.verbose = False - run_cookiecutter(tpl, args, no_input = True) + run_cookiecutter(tpl, args, no_input=True) @patch.object(ArgumentParser, "error")