Release rnasum-pipeline/1.1.0__20240901053225 · umccr/cwl-ica

Overview

MD5Sum: 28bb78f3359e7f977c4be97880886a02

Documentation

Documentation for rnasum-pipeline v1.1.0

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: rnasum_prod__1_1_020240901053225 / Bundle Version 1.1.020240901053225

Description
This bundle has been generated by the release of workflows/rnasum-pipeline/1.1.0/rnasum-pipeline__1.1.0.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/rnasum-pipeline/1.1.0__20240901053225.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is 1.1.0

Bundle ID: 1850ca4f-7df0-4269-968d-5a325ec24611

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 69362d8e-8f6f-4d87-84b5-a8c6205b7032
Pipeline Code: rnasum-pipeline__1_1_0__20240901053225

Projects

development
staging
production

Datasets

rnasum_1_0_0

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/rnasum-pipeline%2F1.1.0__20240901053225/rnasum-pipeline__1.1.0__20240901053225.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--1.1.0/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--1.1.0/run_rnasum_step

Step Type: tool
Docs:

Run the rnasum pipeline

Outputs

Click to expand!

rnasum html

ID: rnasum-pipeline--1.1.0/rnasum_html

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

RNAsum output directory

ID: rnasum-pipeline--1.1.0/rnasum_output_directory

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

rnasum-pipeline/1.1.0__20240901053225

Overview

Documentation

Dockstore

ICAv2

Tenant: umccr-prod

Bundle Name: rnasum_prod__1_1_0__20240901053225 / Bundle Version 1.1.0__20240901053225

Visual Overview

Inputs Template

Yaml

Json

Outputs Template

Overrides Template

Zipped workflow

Packed workflow

Inputs

arriba directory

arriba pdf

arriba tsv

batch rm

cn gain

cn loss

dataset

dataset name incl

dragen fusions

dragen mapping metrics

dragen transcriptome directory

drugs

filter

immunogram

log

manta tsv

norm

PCGR splice vars

pcgr tier

pcgr tiers tsv

project

purple gene tsv

report dir

salmom

sample name

sample source

save tables

scaling

subject id

top genes

transform

umccrise directory

Steps

run rnasum step

Outputs

rnasum html

RNAsum output directory

Bundle Name: rnasum_prod__1_1_020240901053225 / Bundle Version 1.1.020240901053225