From 6291386b92e5cad31b24a6af71cdb2924c809197 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Wed, 7 Jun 2023 15:01:19 +0200 Subject: [PATCH 1/2] fix: make variable naming consistent with ISA standard --- cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json | 2 +- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- cubi_isa_templates/isatab-generic/cookiecutter.json | 4 ++-- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- cubi_isa_templates/isatab-germline/cookiecutter.json | 4 ++-- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- cubi_isa_templates/isatab-microarray/cookiecutter.json | 2 +- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- .../isatab-ms_meta_biocrates/cookiecutter.json | 2 +- ...utter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt | 6 +++--- ...cutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt | 6 +++--- .../s_{{cookiecutter.study_file_name}}.txt | 6 +++--- .../isatab-single_cell_rnaseq/cookiecutter.json | 2 +- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- .../isatab-stem_cell_core_sc/cookiecutter.json | 2 +- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- .../isatab-tumor_normal_triplets/cookiecutter.json | 4 ++-- ...efix}}_transcriptome_profiling_nucleotide_sequencing.txt | 6 +++--- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- 26 files changed, 65 insertions(+), 65 deletions(-) diff --git a/cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json b/cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json index d3c0f73..e14fe38 100644 --- a/cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json +++ b/cubi_isa_templates/isatab-bulk_rnaseq/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "sample1,sample2", + "source_names": "sample1,sample2", "a_measurement_type": [ "transcription profiling" ], diff --git a/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index 9bf9d03..3b79797 100644 --- a/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,5 +1,5 @@ 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 Extract 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}} +{% set source_names = cookiecutter.source_names.split(",") -%} +{% for source_name in source_names -%} +{{source_name|replace("-", "_")}} RNA extraction Library construction Nucleic acid sequencing {{source_name}} {{source_name}} {% endfor -%} diff --git a/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index db09f51..e69eb43 100644 --- a/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-bulk_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,5 +1,5 @@ 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("-", "_")}} +{% set source_names = cookiecutter.source_names.split(",") -%} +{% for source_name in source_names -%} +{{source_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 Sample collection {{source_name|replace("-", "_")}} {% endfor -%} diff --git a/cubi_isa_templates/isatab-generic/cookiecutter.json b/cubi_isa_templates/isatab-generic/cookiecutter.json index dddd96d..e9bc2bb 100644 --- a/cubi_isa_templates/isatab-generic/cookiecutter.json +++ b/cubi_isa_templates/isatab-generic/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "alpha,beta,gamma", + "source_names": "alpha,beta,gamma", "a_measurement_type": [ "transcription profiling" ], @@ -50,7 +50,7 @@ "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", + "source_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" ], diff --git a/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index eef39e2..f826ba7 100644 --- a/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,5 +1,5 @@ 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 Extract 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("-", "_")}} +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{source_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}} {{source_name|replace("-", "_")}}-N1-RNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{source_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 {{source_name|replace("-", "_")}} {% endfor %} diff --git a/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 2a53e22..d2a3842 100644 --- a/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-generic/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,5 +1,5 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}} {{cookiecutter.source_type}}:{{source_name}} {{cookiecutter.batch}} {{cookiecutter.organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}} UNKNOWN UNKNOWN Sample collection {{source_name|replace("-", "_")}}-N1 {% endfor %} diff --git a/cubi_isa_templates/isatab-germline/cookiecutter.json b/cubi_isa_templates/isatab-germline/cookiecutter.json index a029601..e6eb97a 100644 --- a/cubi_isa_templates/isatab-germline/cookiecutter.json +++ b/cubi_isa_templates/isatab-germline/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "index,mother,father", + "source_names": "index,mother,father", "a_measurement_type": [ "exome sequencing", "genome sequencing", @@ -66,7 +66,7 @@ "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", + "source_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", diff --git a/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index b600735..96b8d99 100644 --- a/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,5 +1,5 @@ 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 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 -{% 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{source_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}} {{source_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{source_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 {% endfor %} diff --git a/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 743a787..bf0f34e 100644 --- a/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-germline/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,5 +1,5 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}} {{cookiecutter.source_type}}:{{source_name}} {{cookiecutter.batch}} FAM_{{source_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 0 0 UNKNOWN UNKNOWN Sample collection {{source_name|replace("-", "_")}}-N1 {% endfor %} diff --git a/cubi_isa_templates/isatab-microarray/cookiecutter.json b/cubi_isa_templates/isatab-microarray/cookiecutter.json index 55579b4..7f52194 100644 --- a/cubi_isa_templates/isatab-microarray/cookiecutter.json +++ b/cubi_isa_templates/isatab-microarray/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "alpha,beta,gamma", + "source_names": "alpha,beta,gamma", "a_measurement_type": [ "transcription profiling" ], diff --git a/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index d47c8fc..68df1e8 100644 --- a/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,5 +1,5 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-S1 Nucleic acid extraction {{source_name|replace("-", "_")}}-S1-E1 Labeling Nucleic acid hybridization {{source_name|replace("-", "_")}}-S1-E1-H1 {{cookiecutter.array_design_ref}} Data collection {{source_name|replace("-", "_")}}-S1-E1-H1 Normalization data transformation Data transformation {% endfor %} diff --git a/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 811684b..5b1e8a5 100644 --- a/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-microarray/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,5 +1,5 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}} {{cookiecutter.organisms[cookiecutter.organism].name}} NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/{{cookiecutter.organisms[cookiecutter.organism].taxon}} Sample collection {{source_name|replace("-", "_")}}-S1 day OBI http://purl.obolibrary.org/obo/UO_0000033 {% endfor %} diff --git a/cubi_isa_templates/isatab-ms_meta_biocrates/cookiecutter.json b/cubi_isa_templates/isatab-ms_meta_biocrates/cookiecutter.json index 318a6b1..55dff60 100644 --- a/cubi_isa_templates/isatab-ms_meta_biocrates/cookiecutter.json +++ b/cubi_isa_templates/isatab-ms_meta_biocrates/cookiecutter.json @@ -5,7 +5,7 @@ "study_id": "{{cookiecutter.study_title|lower|replace(' ', '_')}}", "study_file_name": "{{cookiecutter.study_id}}", - "sample_names": "alpha,beta,gamma", + "source_names": "alpha,beta,gamma", "organism": [ "Homo sapiens", diff --git a/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt index 5cc8e4a..7c7f0ca 100644 --- a/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt +++ b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_FIA.txt @@ -1,6 +1,6 @@ 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}} +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} {{source_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}} {{source_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_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt index 50060ff..61c2f49 100644 --- a/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt +++ b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}_LC.txt @@ -1,6 +1,6 @@ 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}} +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Extraction {{cookiecutter.assay_measurement_abbreviation_LC}} {{source_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}} {{source_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_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt index 74e870a..cf889b7 100644 --- a/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt +++ b/cubi_isa_templates/isatab-ms_meta_biocrates/{{cookiecutter.__output_dir}}/s_{{cookiecutter.study_file_name}}.txt @@ -1,6 +1,6 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_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 {{source_name|replace("-", "_")}}-N1 {% endfor %} diff --git a/cubi_isa_templates/isatab-single_cell_rnaseq/cookiecutter.json b/cubi_isa_templates/isatab-single_cell_rnaseq/cookiecutter.json index a9b0842..f6c5419 100644 --- a/cubi_isa_templates/isatab-single_cell_rnaseq/cookiecutter.json +++ b/cubi_isa_templates/isatab-single_cell_rnaseq/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "sample1,sample2", + "source_names": "sample1,sample2", "a_measurement_type": "transcription profiling", "lib_kit": [ "SC3Pv3", diff --git a/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index 089cb9e..6782c9d 100644 --- a/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,14 +1,14 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} +{% set source_names = cookiecutter.source_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 Extract Name -{% for sample_name in sample_names -%} +{% for source_name in source_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}} +{{source_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 %} {{source_name}}_{{abr}} Nucleic acid sequencing {{source_name}}_{{abr}} {%+ for meta in sequencing_meta %} {% endfor %} {{source_name}} {% endfor -%} {% endfor -%} diff --git a/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 88778d0..2a964bb 100644 --- a/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-single_cell_rnaseq/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,7 +1,7 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} +{% set source_names = cookiecutter.source_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 %} +{% for source_name in source_names -%} +{{source_name|replace("-", "_")}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606{%+ for meta in source_meta %} {% endfor %} Sample collection {{source_name|replace("-", "_")}}{%+ for meta in sample_meta %} {% endfor %} {% endfor -%} diff --git a/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json b/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json index 1b56b3b..0f54fa4 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json @@ -1,7 +1,7 @@ { "group": "CoreRnD", "study_title": "Study Title", - "sample_names": "sample1,sample2", + "source_names": "sample1,sample2", "investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", "source_type": ["hiPSC", "tissue"], "cellline": "BIHiXXX-Y", diff --git a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index 8d5770e..1071067 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,15 +1,15 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} +{% set source_names = cookiecutter.source_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 Extract Name -{% for sample_name in sample_names -%} +{% for source_name in source_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(" ", "_") -%} +{% set sample = source_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_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 8eaa781..873aa60 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,8 +1,8 @@ -{% set sample_names = cookiecutter.sample_names.split(",") -%} +{% set source_names = cookiecutter.source_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(" ", "_") -%} +{% for source_name in source_names -%} +{% set sample = source_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_isa_templates/isatab-tumor_normal_triplets/cookiecutter.json b/cubi_isa_templates/isatab-tumor_normal_triplets/cookiecutter.json index f69c36d..f228c27 100644 --- a/cubi_isa_templates/isatab-tumor_normal_triplets/cookiecutter.json +++ b/cubi_isa_templates/isatab-tumor_normal_triplets/cookiecutter.json @@ -1,6 +1,6 @@ { "investigation_title": "Investigation Title", - "sample_names": "normal,tumor", + "source_names": "normal,tumor", "a_measurement_type": [ "exome sequencing", "genome sequencing", @@ -61,7 +61,7 @@ "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", + "source_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": [ diff --git a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt index 7ce23e4..9ace08f 100644 --- a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt +++ b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_transcriptome_profiling_nucleotide_sequencing.txt @@ -1,5 +1,5 @@ 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 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[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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction RNA-Seq {{source_name|replace("-", "_")}}-N1-RNA1 Library construction RNA-Seq TRANSCRIPTOMIC RNA-Seq PolyA PAIRED Illumina TruSeq Stranded mRNA REVERSE {{source_name|replace("-", "_")}}-N1-RNA1-RNA-Seq1 {{source_name}} Nucleic acid sequencing RNA-Seq ILLUMINA Illumina HiSeq 4000 Phred+33 {% endfor %} diff --git a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index ee1e705..336ce7c 100644 --- a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,5 +1,5 @@ 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 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[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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}}-N1 Nucleic acid extraction {{cookiecutter.a_measurement_abbreviation}} {{source_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}} {{source_name|replace("-", "_")}}-N1-DNA1-{{cookiecutter.a_measurement_abbreviation}}1 {{source_name}} Nucleic acid sequencing {{cookiecutter.a_measurement_abbreviation}} ILLUMINA {{cookiecutter.instrument}} Phred+33 {% endfor %} diff --git a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 49431b9..6c7607a 100644 --- a/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-tumor_normal_triplets/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,5 +1,5 @@ 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 +{% set source_names = cookiecutter.source_names.split(",") -%} +{%- for source_name in source_names -%} +{{source_name|replace("-", "_")}} {{cookiecutter.source_type}}:{{source_name}} Homo sapiens NCBITAXON http://purl.bioontology.org/ontology/NCBITAXON/9606 none Sample collection {{source_name|replace("-", "_")}}-N1 Y/N True/False {% endfor %} From 9272559a751649c0c89a8e67d65f16f954f9e0c8 Mon Sep 17 00:00:00 2001 From: Thomas Sell Date: Thu, 15 Jun 2023 10:29:32 +0200 Subject: [PATCH 2/2] revert changes to stem_cell_core_sc template --- .../isatab-stem_cell_core_sc/cookiecutter.json | 2 +- ...kiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt | 6 +++--- .../s_{{cookiecutter.s_file_name}}.txt | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json b/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json index 0f54fa4..1b56b3b 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/cookiecutter.json @@ -1,7 +1,7 @@ { "group": "CoreRnD", "study_title": "Study Title", - "source_names": "sample1,sample2", + "sample_names": "sample1,sample2", "investigation_title": "{{cookiecutter.group}} - {{cookiecutter.study_title}}", "source_type": ["hiPSC", "tissue"], "cellline": "BIHiXXX-Y", diff --git a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt index 1071067..8d5770e 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/a_{{cookiecutter.assay_prefix}}_{{cookiecutter.assay_name}}.txt @@ -1,15 +1,15 @@ -{% set source_names = cookiecutter.source_names.split(",") -%} +{% 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 Extract Name -{% for source_name in source_names -%} +{% 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 = source_name|replace(" ", "_") -%} +{% 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_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt index 873aa60..8eaa781 100644 --- a/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt +++ b/cubi_isa_templates/isatab-stem_cell_core_sc/{{cookiecutter.__output_dir}}/s_{{cookiecutter.s_file_name}}.txt @@ -1,8 +1,8 @@ -{% set source_names = cookiecutter.source_names.split(",") -%} +{% 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 source_name in source_names -%} -{% set sample = source_name|replace(" ", "_") -%} +{% 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 -%}