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@github-actions github-actions released this 27 Jun 06:02
· 257 commits to main since this release
rnasum-pipeline/1.0.0__20240627060107
c4a03f8

Overview

MD5Sum: 4f9161e89c88ccc5da02935d1d1d0df9

Documentation

Documentation for rnasum-pipeline v1.0.0

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: rnasum_prod__1_0_0__20240627060107 / Bundle Version v9_r3__20240627060107

Description
This bundle has been generated by the release of workflows/rnasum-pipeline/1.0.0/rnasum-pipeline__1.0.0.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/rnasum-pipeline/1.0.0__20240627060107.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3

Bundle ID: 8ccc93cb-1928-49c7-8695-24140a3293e0

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: bd6e5690-3ccf-4ac4-997d-59462f852f65
    Pipeline Code: rnasum-pipeline__1_0_0__20240627060107

Projects

  • development
  • staging
  • production

Datasets

  • rnasum_1_0_0

Visual Overview

Click to expand!

rnasum-pipeline

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/rnasum-pipeline%2F1.0.0__20240627060107/rnasum-pipeline__1.0.0__20240627060107.schema.json

# arriba directory (Optional)
# Docs: Location of the arriba outputs directory
arriba_dir:
  class: Directory
  location: icav2://project_id/path/to/dir/

# arriba pdf (Optional)
# Docs: Location of the pdf output from arriba
arriba_pdf:
  class: File
  location: icav2://project_id/path/to/file

# arriba tsv (Optional)
# Docs: Location of the tsv output from arriba
arriba_tsv:
  class: File
  location: icav2://project_id/path/to/file

# batch rm (Optional)
# Default value: True
# Docs: Remove batch-associated effects between datasets. Available options are: "TRUE" (default) and "FALSE"
batch_rm: true

# cn gain (Optional)
# Default value: 95
# Docs: CN threshold value to classify genes within gained regions.
cn_gain: 95

# cn loss (Optional)
# Default value: 5
# Docs: CN threshold value to classify genes within lost regions.
cn_loss: 5

# dataset (Optional)
# Default value: PANCAN
# Docs: Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md
dataset: "PANCAN"

# dataset name incl (Optional)
# Docs: Include dataset in the report and sample name.
dataset_name_incl: false

# dragen fusions (Optional)
# Docs: Location of the fusion output from Dragen RNA-seq pipeline
dragen_fusions:
  class: File
  location: icav2://project_id/path/to/file

# dragen mapping metrics (Optional)
# Docs: Location of the mapping metrics from Dragen RNA-seq pipeline
dragen_mapping_metrics:
  class: File
  location: icav2://project_id/path/to/file

# dragen transcriptome directory (Optional)
# Docs: Location of the results from Dragen RNA-seq pipeline
dragen_wts_dir:
  class: Directory
  location: icav2://project_id/path/to/dir/

# drugs (Optional)
# Docs: Include drug matching section in the report.
drugs: false

# filter (Optional)
# Default value: True
# Docs: Filtering out low expressed genes. Available options are: "TRUE" (default) and "FALSE"
filter: true

# immunogram (Optional)
# Docs: Include drug matching section in the report.
immunogram: false

# log (Optional)
# Default value: True
# Docs: Log (base 2) transform data before normalisation. Available options are: "TRUE" (default) and "FALSE"
log: true

# manta tsv (Optional)
# Docs: Location of the tsv output from manta
manta_tsv:
  class: File
  location: icav2://project_id/path/to/file

# norm (Optional)
# Default value: TMM
# Docs: Normalisation method
norm: "TMM"

# PCGR splice vars (Optional)
# Default value: True
# Docs: Include non-coding splice region variants reported in PCGR. Available options are: "TRUE" (default) and "FALSE"
pcgr_splice_vars: true

# pcgr tier (Optional)
# Default value: 4
# Docs: Tier threshold for reporting variants reported in PCGR.
pcgr_tier: 4

# pcgr tiers tsv (Optional)
# Docs: Location of the tsv output from pcgr
pcgr_tiers_tsv:
  class: File
  location: icav2://project_id/path/to/file

# project (Optional)
# Docs: Project name. This information is for annotation purposes only
project: string

# purple gene tsv (Optional)
# Docs: Location of the tsv output from purple
purple_gene_tsv:
  class: File
  location: icav2://project_id/path/to/file

# report dir (Required)
# Docs: Desired location for the outputs
report_dir: string

# salmom (Optional)
# Docs: Location of the quantification output from salmon
salmon:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: Desired sample name to be presented in the report
sample_name: string

# sample source (Optional)
# Docs: Source of investigated sample (e.g. fresh frozen tissue, organoid).
# This information is for annotation purposes only
sample_source: string

# save tables (Optional)
# Default value: True
# Docs: Save interactive summary tables as HTML. Available options are: "TRUE" (default) and "FALSE"
save_tables: true

# scaling (Optional)
# Default value: gene-wise
# Docs: Apply "gene-wise" (default) or "group-wise" data scaling
scaling: "gene-wise"

# subject id (Optional)
# Docs: Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID 
# is extracted from there and used to overwrite this argument.
subject_id: string

# top genes (Optional)
# Default value: 5
# Docs: The number of top ranked genes to be presented.
top_genes: 5

# transform (Optional)
# Default value: CPM
# Docs: Transformation method to be used when converting read counts
transform: "CPM"

# umccrise directory (Optional)
# Docs: The umccrise output directory
umccrise:
  class: Directory
  location: icav2://project_id/path/to/dir/

Json

Click to expand! 
{
    "arriba_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "arriba_pdf": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "arriba_tsv": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "batch_rm": true,
    "cn_gain": 95,
    "cn_loss": 5,
    "dataset": "PANCAN",
    "dataset_name_incl": false,
    "dragen_fusions": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "dragen_mapping_metrics": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "dragen_wts_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "drugs": false,
    "filter": true,
    "immunogram": false,
    "log": true,
    "manta_tsv": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "norm": "TMM",
    "pcgr_splice_vars": true,
    "pcgr_tier": 4,
    "pcgr_tiers_tsv": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "project": "string",
    "purple_gene_tsv": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "report_dir": "string",
    "salmon": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "sample_name": "string",
    "sample_source": "string",
    "save_tables": true,
    "scaling": "gene-wise",
    "subject_id": "string",
    "top_genes": 5,
    "transform": "CPM",
    "umccrise": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Outputs Template

Click to expand! 
{
    "rnasum_html": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "rnasum_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand! 
[
    "workflow.cwl#rnasum-pipeline--1.0.0/run_rnasum_step"
]

Packed workflow

Click to expand! 
[
    "#main/run_rnasum_step"
]

Inputs

Click to expand!

arriba directory

ID: arriba_dir

Optional: True
Type: Directory
Docs:
Location of the arriba outputs directory

arriba pdf

ID: arriba_pdf

Optional: True
Type: File
Docs:
Location of the pdf output from arriba

arriba tsv

ID: arriba_tsv

Optional: True
Type: File
Docs:
Location of the tsv output from arriba

batch rm

ID: batch_rm

Optional: True
Type: boolean
Docs:
Remove batch-associated effects between datasets. Available options are: "TRUE" (default) and "FALSE"

cn gain

ID: cn_gain

Optional: True
Type: int
Docs:
CN threshold value to classify genes within gained regions.

cn loss

ID: cn_loss

Optional: True
Type: int
Docs:
CN threshold value to classify genes within lost regions.

dataset

ID: dataset

Optional: False
Type: string
Docs:
Reference dataset selection from https://github.com/umccr/RNAsum/blob/master/TCGA_projects_summary.md

dataset name incl

ID: dataset_name_incl

Optional: True
Type: boolean
Docs:
Include dataset in the report and sample name.

dragen fusions

ID: dragen_fusions

Optional: True
Type: File
Docs:
Location of the fusion output from Dragen RNA-seq pipeline

dragen mapping metrics

ID: dragen_mapping_metrics

Optional: True
Type: File
Docs:
Location of the mapping metrics from Dragen RNA-seq pipeline

dragen transcriptome directory

ID: dragen_wts_dir

Optional: True
Type: Directory
Docs:
Location of the results from Dragen RNA-seq pipeline

drugs

ID: drugs

Optional: True
Type: boolean
Docs:
Include drug matching section in the report.

filter

ID: filter

Optional: True
Type: boolean
Docs:
Filtering out low expressed genes. Available options are: "TRUE" (default) and "FALSE"

immunogram

ID: immunogram

Optional: True
Type: boolean
Docs:
Include drug matching section in the report.

log

ID: log

Optional: True
Type: boolean
Docs:
Log (base 2) transform data before normalisation. Available options are: "TRUE" (default) and "FALSE"

manta tsv

ID: manta_tsv

Optional: True
Type: File
Docs:
Location of the tsv output from manta

norm

ID: norm

Optional: True
Type: string
Docs:
Normalisation method

PCGR splice vars

ID: pcgr_splice_vars

Optional: True
Type: boolean
Docs:
Include non-coding splice region variants reported in PCGR. Available options are: "TRUE" (default) and "FALSE"

pcgr tier

ID: pcgr_tier

Optional: True
Type: int
Docs:
Tier threshold for reporting variants reported in PCGR.

pcgr tiers tsv

ID: pcgr_tiers_tsv

Optional: True
Type: File
Docs:
Location of the tsv output from pcgr

project

ID: project

Optional: True
Type: string
Docs:
Project name. This information is for annotation purposes only

purple gene tsv

ID: purple_gene_tsv

Optional: True
Type: File
Docs:
Location of the tsv output from purple

report dir

ID: report_dir

Optional: False
Type: string
Docs:
Desired location for the outputs

salmom

ID: salmon

Optional: True
Type: File
Docs:
Location of the quantification output from salmon

sample name

ID: sample_name

Optional: False
Type: string
Docs:
Desired sample name to be presented in the report

sample source

ID: sample_source

Optional: True
Type: string
Docs:
Source of investigated sample (e.g. fresh frozen tissue, organoid).
This information is for annotation purposes only

save tables

ID: save_tables

Optional: True
Type: boolean
Docs:
Save interactive summary tables as HTML. Available options are: "TRUE" (default) and "FALSE"

scaling

ID: scaling

Optional: True
Type: string
Docs:
Apply "gene-wise" (default) or "group-wise" data scaling

subject id

ID: subject_id

Optional: True
Type: string
Docs:
Subject ID. If umccrise output is specified (flag --umccrise) then Subject ID
is extracted from there and used to overwrite this argument.

top genes

ID: top_genes

Optional: True
Type: int
Docs:
The number of top ranked genes to be presented.

transform

ID: transform

Optional: True
Type: string
Docs:
Transformation method to be used when converting read counts

umccrise directory

ID: umccrise

Optional: True
Type: Directory
Docs:
The umccrise output directory

Steps

Click to expand!

run rnasum step

ID: rnasum-pipeline--1.0.0/run_rnasum_step

Step Type: tool
Docs:

Run the rnasum pipeline

Outputs

Click to expand!

rnasum html

ID: rnasum-pipeline--1.0.0/rnasum_html

Optional: False
Output Type: File
Docs:
The HTML report output of RNAsum

RNAsum output directory

ID: rnasum-pipeline--1.0.0/rnasum_output_directory

Optional: False
Output Type: Directory
Docs:
Output directory containing all outputs of the RNAsum run

Assets 10
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