Releases · umccr/cwl-ica

30 Oct 04:21

github-actions

dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241030041958

06454f3

dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241030041958 Latest

Latest

Overview

MD5Sum: da57d2421f8ffb47ec102dd02a4d5db7

Documentation

This tool can be used for archiving purposes by first compressing fastqs prior to transfer to a long-term storage location.

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: ora_instrument_run_compression_pipeline_with_reference__4_2_420241030041958 / Bundle Version v220241030041958

Description
This bundle has been generated by the release of workflows/dragen-instrument-run-fastq-to-ora-pipeline/4.2.4/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241030041958.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v2

Bundle ID: 21a15230-7927-4c07-ad9c-05b0c2b11b66

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: ba8f618a-842f-4a2f-9b2f-a074c0472218
Pipeline Code: dragen-instrument-run-fastq-to-ora-pipeline__4_2_4__20241030041958

Projects

development
staging
production

Datasets

ora-reference-v2

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-instrument-run-fastq-to-ora-pipeline%2F4.2.4__20241030041958/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241030041958.schema.json

# instrument run directory (Required)
# Docs: The directory containing the instrument run. Expected to be in the BCLConvert 4.2.7 output format, with the following structure:
#   Reports/
#   InterOp/
#   Logs/
#   Samples/
#   Samples/Lane_1/
#   Samples/Lane_1/Sample_ID/
#   Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R1_001.fastq.gz
#   Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R2_001.fastq.gz
#   etc...
instrument_run_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# ora check file integrity (Optional)
# Default value: False
# Docs: Set to true to perform and output result of FASTQ file and decompressed FASTQ.ORA integrity check. The default value is false.
ora_check_file_integrity: false

# ora parallel files (Optional)
# Default value: 2
# Docs: The number of files to compress in parallel. If using an FPGA medium instance in the 
# run_dragen_instrument_run_fastq_to_ora_step this should be set to 16 / ora_threads_per_file.
ora_parallel_files: 2

# ora print file info (Optional)
# Default value: False
# Docs: Prints file information summary of ORA compressed files.
ora_print_file_info: false

# ora reference (Required)
# Docs: The reference tar to use for the ORA compression
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# ora threads per file (Optional)
# Default value: 8
# Docs: The number of threads to use per file. If using an FPGA medium instance in the 
# run_dragen_instrument_run_fastq_to_ora_step this should be set to 4 since there are only 16 cores available
ora_threads_per_file: 8

# sample id list (Optional)
# Docs: Optional list of samples to process.  
# Samples NOT in this list are NOT compressed AND NOT transferred to the final output directory!
sample_id_list:
- string

Json

Click to expand!

{
    "instrument_run_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "ora_check_file_integrity": false,
    "ora_parallel_files": 2,
    "ora_print_file_info": false,
    "ora_reference": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "ora_threads_per_file": 8,
    "sample_id_list": [
        "string"
    ]
}

Outputs Template

Click to expand!

{
    "output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand!

[
    "workflow.cwl#dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/run_dragen_instrument_run_fastq_to_ora_step"
]

Packed workflow

Click to expand!

[
    "#main/run_dragen_instrument_run_fastq_to_ora_step"
]

Inputs

Click to expand!

instrument run directory

ID: instrument_run_directory

Optional: False
Type: Directory
Docs:
The directory containing the instrument run. Expected to be in the BCLConvert 4.2.7 output format, with the following structure:
Reports/
InterOp/
Logs/
Samples/
Samples/Lane_1/
Samples/Lane_1/Sample_ID/
Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R1_001.fastq.gz
Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R2_001.fastq.gz
etc...

ora check file integrity

ID: ora_check_file_integrity

Optional: False
Type: boolean
Docs:
Set to true to perform and output result of FASTQ file and decompressed FASTQ.ORA integrity check. The default value is false.

ora parallel files

ID: ora_parallel_files

Optional: True
Type: int
Docs:
The number of files to compress in parallel. If using an FPGA medium instance in the
run_dragen_instrument_run_fastq_to_ora_step this should be set to 16 / ora_threads_per_file.

ora print file info

ID: ora_print_file_info

Optional: False
Type: boolean
Docs:
Prints file information summary of ORA compressed files.

ora reference

ID: ora_reference

Optional: False
Type: File
Docs:
The reference tar to use for the ORA compression

ora threads per file

ID: ora_threads_per_file

Optional: True
Type: int
Docs:
The number of threads to use per file. If using an FPGA medium instance in the
run_dragen_instrument_run_fastq_to_ora_step this should be set to 4 since there are only 16 cores available

sample id list

ID: sample_id_list

Optional: True
Type: .[]
Docs:
Optional list of samples to process.
Samples NOT in this list are NOT compressed AND NOT transferred to the final output directory!

Steps

Click to expand!

Run Dragen Instrument Run Fastq to ORA

ID: dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/run_dragen_instrument_run_fastq_to_ora_step

Step Type: tool
Docs:

Run the dragen instrument run fastq to ora tool

Outputs

Click to expand!

output directory

ID: dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/output_directory

Optional: False
Output Type: Directory
Docs:
The output directory of the instrument run with fastqs converted to oras

Assets 10

01 Sep 05:34

github-actions

rnasum-pipeline/1.1.0__20240901053225

451c028

rnasum-pipeline/1.1.0__20240901053225

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_in...

Assets 10

30 Aug 04:13

github-actions

dragen-wts-qc-pipeline/4.2.4__20240830041140

14b6175

dragen-wts-qc-pipeline/4.2.4__20240830041140

Overview

MD5Sum: 734930b3b2ef27e53799d54e9c47e37d

Documentation

Documentation for dragen-wts-qc-pipeline v4.2.4

Dockstore

Dockstore Version Link

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-wts-qc-pipeline%2F4.2.4__20240830041140/dragen-wts-qc-pipeline__4.2.4__20240830041140.schema.json

# algorithm (Optional)
# Default value: proportional
# Docs: Counting algorithm:
# uniquely-mapped-reads(default) or proportional.
algorithm: "proportional"

# annotation file (Required)
# Docs: Path to annotation transcript file.
annotation_file:
  class: File
  location: icav2://project_id/path/to/file

# bam input (Optional)
# Docs: Input a BAM file for WTS analysis
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# enable duplicate marking (Required)
# Docs: Mark identical alignments as duplicates
enable_duplicate_marking: false

# enable map align (Optional)
# Docs: Enabled by default.
# Set this value to false if using bam_input AND tumor_bam_input
enable_map_align: false

# enable map align output (Required)
# Docs: Do you wish to have the output bam files present
enable_map_align_output: false

# enable rna gene fusion (Optional)
# Docs: Optional - Enable the DRAGEN Gene Fusion module - defaults to true
enable_rna_gene_fusion: false

# enable rna quantification (Optional)
# Docs: Optional - Enable the quantification module - defaults to true
enable_rna_quantification: false

# enable sort (Optional)
# Docs: True by default, only set this to false if using --bam-input as input parameter
enable_sort: false

# fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files
# to process. read_1 and read_2 components in the CSV file must be presigned urls.
fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# java mem (Optional)
# Default value: 96G
# Docs: Set desired Java heap memory size
java_mem: "96G"

# license instance id location (Optional)
# Docs: You may wish to place your own in.
# Optional value, default set to /opt/instance-identity
# which is a path inside the dragen container
lic_instance_id_location:
  class: File
  location: icav2://project_id/path/to/file

# output directory (Required)
# Docs: The directory where all output files are placed
output_directory: string

# output file prefix (Required)
# Docs: The prefix given to all output files
output_file_prefix: string

# reference tar (Required)
# Docs: Path to ref data tarball
reference_tar:
  class: File
  location: icav2://project_id/path/to/file

Json

Click to expand!

{
    "algorithm": "proportional",
    "annotation_file": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "bam_input": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "enable_duplicate_marking": false,
    "enable_map_align": false,
    "enable_map_align_output": false,
    "enable_rna_gene_fusion": false,
    "enable_rna_quantification": false,
    "enable_sort": false,
    "fastq_list": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "fastq_list_rows": [
        {
            "rgid": "string",
            "rglb": "string",
            "rgsm": "string",
            "lane": "string",
            "read_1": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            },
            "read_2": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            }
        }
    ],
    "java_mem": "96G",
    "lic_instance_id_location": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "output_directory": "string",
    "output_file_prefix": "string",
    "reference_tar": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    }
}

Outputs Template

Click to expand!

{
    "dragen_transcriptome_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "qualimap_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand!

[
    "workflow.cwl#dragen-wts-qc-pipeline--4.2.4/run_dragen_transcriptome_step",
    "workflow.cwl#dragen-wts-qc-pipeline--4.2.4/run_qualimap_step"
]

Packed workflow

Click to expand!

[
    "#main/run_dragen_transcriptome_step",
    "#main/run_qualimap_step"
]

Inputs

Click to expand!

algorithm

ID: algorithm

Optional: True
Type: string
Docs:
Counting algorithm:
uniquely-mapped-reads(default) or proportional.

annotation file

ID: annotation_file

Optional: False
Type: File
Docs:
Path to annotation transcript file.

bam input

ID: bam_input

Optional: True
Type: File
Docs:
Input a BAM file for WTS analysis

enable duplicate marking

ID: enable_duplicate_marking

Optional: False
Type: boolean
Docs:
Mark identical alignments as duplicates

enable map align

ID: enable_map_align

Optional: True
Type: boolean
Docs:
Enabled by default.
Set this value to false if using bam_input AND tumor_bam_input

enable map align output

ID: enable_map_align_output

Optional: False
Type: boolean
Docs:
Do you wish to have the output bam files present

enable rna gene fusion

ID: enable_rna_gene_fusion

Optional: True
Type: boolean
Docs:
Optional - Enable the DRAGEN Gene Fusion module - defaults to true

enable rna quantification

ID: enable_rna_quantification

Optional: True
Type: boolean
Docs:
Optional - Enable the quantification module - defaults to true

enable sort

ID: enable_sort

Optional: True
Type: boolean
Docs:
True by default, only set this to false if using --bam-input as input parameter

fastq list

ID: fastq_list

Optional: True
Type: File
Docs:
CSV file that contains a list of FASTQ files
to process. read_1 and read_2 components in the CSV file must be presigned urls.

Row of fastq lists

ID: fastq_list_rows

Optional: True
Type: fastq-list-row[]
Docs:
The row of fastq lists.
Each row has the following attributes:

RGID
RGLB
RGSM
Lane
Read1File
Read2File (optional)

java mem

ID: java_mem

Optional: True
Type: string
Docs:
Set desired Java heap memory size

license instance id location

ID: lic_instance_id_location

Optional: True
Type: ['File', 'string']
Docs:
You may wish to place your own in.
Optional value, default set to /opt/instance-identity
which is a path inside the dragen container

output directory

ID: output_directory

Optional: False
Type: string
Docs:
The directory where all output files are placed

output file prefix

ID: output_file_prefix

Optional: False
Type: string
Docs:
The prefix given to all output files

reference tar

ID: reference_tar

Optional: False
Type: File
Docs:
Path to ref data tarball

Steps

Click to expand!

run dragen transcriptome step

ID: dragen-wts-qc-pipeline--4.2.4/run_dragen_transcriptome_step

Step Type: tool
Docs:

Runs the dragen transcriptome workflow on the FPGA.
Takes in a fastq list and corresponding mount paths from the predefined_mount_paths.
All other options avaiable at the top of the workflow

run qualimap step

ID: dragen-wts-qc-pipeline--4.2.4/run_qualimap_step

Step Type: tool
Docs:

Run qualimap step to generate additional QC metrics

Outputs

Click to expand!

dragen transcriptome output directory

ID: dragen-wts-qc-pipeline--4.2.4/dragen_transcriptome_output_directory

Optional: False
Output Type: Directory
Docs:
The output directory containing all transcriptome output files

dragen transcriptome output directory

ID: dragen-wts-qc-pipeline--4.2.4/qualimap_output_directory

Optional: False
Output Type: Directory
Docs:
The output directory containing all transcriptome output files

Assets 10

30 Aug 04:20

github-actions

dragen-transcriptome-pipeline/4.2.4__20240830041834

1e7ba27

dragen-transcriptome-pipeline/4.2.4__20240830041834

Overview

MD5Sum: d8bbfbee2f713b2ea768d5ea8a8285b9

Documentation

Documentation for dragen-transcriptome-pipeline v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_transcriptome_pipeline_with_validation_data__4_2_4__20240830041834 / Bundle Version v9_r3__20240830041834

Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240830041834.

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

Bundle ID: dbf1f105-23a6-4b00-9b7a-a9412f50f274

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 1e53ae07-08a6-458b-9fa3-9cf7430409a0
Pipeline Code: dragen-transcriptome-pipeline__4_2_4__20240830041834

Projects

development
staging

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_fasta
arriba_2_4_0
hg38_v39_gencode_annotation
wts_validation_fastq__SBJ00480
wts_validation_fastq__SBJ00028
wts_validation_fastq__SBJ00061
wts_validation_fastq__SBJ00188
wts_validation_fastq__SBJ00199
wts_validation_fastq__SBJ00236
wts_validation_fastq__SBJ00238
wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563
wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147
wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620
wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286
wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673

Bundle Name: dragen_transcriptome_pipeline_prod__4_2_4__20240830041834 / Bundle Version v9_r3__20240830041834

Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240830041834.

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

Bundle ID: e70dac7e-23c7-4e52-9cff-16a65640afcb

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 1e53ae07-08a6-458b-9fa3-9cf7430409a0
Pipeline Code: dragen-transcriptome-pipeline__4_2_4__20240830041834

Projects

production

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_fasta
arriba_2_4_0
hg38_v39_gencode_annotation
wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563
wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147
wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620
wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286
wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-transcriptome-pipeline%2F4.2.4__20240830041834/dragen-transcriptome-pipeline__4.2.4__20240830041834.schema.json

# algorithm (Optional)
# Default value: proportional
# Docs: Counting algorithm:
# uniquely-mapped-reads(default) or proportional.
algorithm: "proportional"

# annotation file (Required)
# Docs: Path to annotation transcript file.
annotation_file:
  class: File
  location: icav2://project_id/path/to/file

# bam input (Optional)
# Docs: Input a BAM file for WTS analysis
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# blacklist (Required)
# Docs: File with blacklist range
blacklist:
  class: File
  location: icav2://project_id/path/to/file

# cl config (Optional)
# Docs: command line config to supply additional config values on the command line.
cl_config: string

# contigs (Optional)
# Docs: Optional - List of interesting contigs
# If not specified, defaults to 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
contigs: string

# cytobands (Required)
# Docs: Coordinates of the Giemsa staining bands.
cytobands:
  class: File
  location: icav2://project_id/path/to/file

# enable duplicate marking (Required)
# Docs: Mark identical alignments as duplicates
enable_duplicate_marking: false

# enable map align (Optional)
# Docs: Enabled by default.
# Set this value to false if using bam_input AND tumor_bam_input
enable_map_align: false

# enable map align output (Required)
# Docs: Do you wish to have the output bam files present
enable_map_align_output: false

# enable rna gene fusion (Optional)
# Docs: Optional - Enable the DRAGEN Gene Fusion module - defaults to true
enable_rna_gene_fusion: false

# enable rna quantification (Optional)
# Docs: Optional - Enable the quantification module - defaults to true
enable_rna_quantification: false

# enable sort (Optional)
# Docs: True by default, only set this to false if using --bam-input as input parameter
enable_sort: false

# fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files
# to process. read_1 and read_2 components in the CSV file must be presigned urls.
fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# java mem (Optional)
# Default value: 20G
# Docs: Set desired Java heap memory size
java_mem: "20G"

# license instance id location (Optional)
# Docs: You may wish to place your own in.
# Optional value, default set to /opt/instance-identity
# which is a path inside the dragen container
lic_instance_id_location:
  class: File
  location: icav2://project_id/path/to/file

# output file prefix (Required)
# Docs: The prefix given to all output files
output_prefix: string

# protein domains (Required)
# Docs: GFF3 file containing the genomic coordinates of protein domains.
protein_domains:
  class: File
  location: icav2://project_id/path/to/file

# qc reference samples (Required)
# Docs: Reference samples for multiQC report
qc_reference_samples:
- class: Directory
  location: icav2://project_id/path/to/dir/

# read trimming (Optional)
# Docs: To enable trimming filters in hard-trimming mode, set to a comma-separated list of the trimmer tools 
# you would like to use. To disable trimming, set to none. During mapping, artifacts are removed from all reads.
# Read trimming is disabled by default.
read_trimmers: string

# reference Fasta (Required)
# Docs: FastA file with genome sequence
reference_fasta:
  class: File
  location: icav2://project_id/path/to/file

# reference tar (Required)
# Docs: Path to ref data tarball
reference_tar:
  class: File
  location: icav2://project_id/path/to/file

# soft read trimming (Optional)
# Docs: To enable trimming filters in soft-trimming mode, set to a comma-separated list of the trimmer tools 
# you would like to use. To disable soft trimming, set to none. During mapping, reads are aligned as if trimmed,
# and bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.
soft_read_trimmers: string

# trim adapter r1 5prime (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 1. 
# NB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.
trim_adapter_r1_5prime:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter read1 (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 1.
trim_adapter_read1:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter read2 (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 2.
trim_adapter_read2:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter stringency (Optional)
# Docs: Specify the minimum number of adapter bases required for trimming
trim_adapter_stringency: string

# trim adapter r2 5prime (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 2.
# NB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.
trim_dapter_r2_5prime:
  class: File
  location: icav2://project_id/path/to/file

# trim r1 3prime (Optional)
# Docs: Specify the minimum number of bases to trim from the 3' end of Read 1 (default: 0).
trim_r1_3prime: string

# trim r1 5prime (Optional)
# Docs: Specify the minimum number of bases to trim from the 5' end of Read 1 (default: 0).
trim_r1_5prime: string

# trim r2 3prime (Optional)
# Docs: Specify the minimum number of bases to trim from the 3' end of Read 2 (default: 0).
trim_r2_3prime: string

# trim r2 5prime (Optional)
# Docs: Specify the minimum number of bases to trim...

Assets 10

30 Aug 04:14

github-actions

dragen-somatic-with-germline-pipeline/4.2.4__20240830041201

1b1de28

dragen-somatic-with-germline-pipeline/4.2.4__20240830041201

Overview

MD5Sum: a9d59f7474a1b87d531c2a859a29316d

Documentation

Documentation for dragen-somatic-with-germline-pipeline
v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_2_4__20240830041201 / Bundle Version v9_r3__20240830041201

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240830041201.

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

Bundle ID: 1288012a-b0dd-4ccd-bc2a-576fad2f7f0d

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 0f5575bc-6cf8-4a90-a80e-05088aae8ed7
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240830041201

Projects

development
staging

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
wgs_validation_fastq__cups_pair_8
wgs_validation_fastq__2016_249_17_MH_P033
wgs_validation_fastq__2016_249_18_WH_P025
wgs_validation_fastq__B_ALL_Case_10
wgs_validation_fastq_Diploid_Never_Responder
wgs_validation_fastq_SBJ00303
wgs_validation_fastq_SEQC50
wgs_validation_fastq_SFRC01073

Bundle Name: dragen_somatic_with_germline_pipeline_prod__4_2_4__20240830041201 / Bundle Version v9_r3__20240830041201

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240830041201.

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

Bundle ID: 71297be1-5180-4f64-ac0e-2846a0a51e56

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 0f5575bc-6cf8-4a90-a80e-05088aae8ed7
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240830041201

Projects

production

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-somatic-with-germline-pipeline%2F4.2.4__20240830041201/dragen-somatic-with-germline-pipeline__4.2.4__20240830041201.schema.json

# bam input (Optional)
# Docs: Input a normal BAM file for the variant calling stage
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# cnv enable self normalization (Optional)
# Docs: Enable CNV self normalization.
# Self Normalization requires that the DRAGEN hash table be generated with the enable-cnv=true option.
cnv_enable_self_normalization: false

# cnv normal b allele vcf (Optional)
# Docs: Specify a matched normal SNV VCF.
cnv_normal_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv normal cnv vcf (Optional)
# Docs: Specify germline CNVs from the matched normal sample.
cnv_normal_cnv_vcf: false

# cnv population b allele vcf (Optional)
# Docs: Specify a population SNP catalog.
cnv_population_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv somatic enable het calling (Optional)
# Docs: Enable HET-calling mode for heterogeneous segments.
cnv_somatic_enable_het_calling: false

# cnv somatic enable lower ploidy limit (Optional)
# Docs: To improve accuracy on the tumor ploidy model estimation, the somatic WGS CNV caller estimates whether the chosen model calls 
# homozygous deletions on regions that are likely to reduce the overall fitness of cells, 
# which are therefore deemed to be "essential" and under negative selection. 
# In the current literature, recent efforts tried to map such cell-essential genes (eg, in 2015 - https://www.science.org/doi/10.1126/science.aac7041).
# The check on essential regions is controlled with --cnv-somatic-enable-lower-ploidy-limit (default true).
cnv_somatic_enable_lower_ploidy_limit: false

# cnv somatic essential genes bed (Optional)
# Docs: Default bedfiles describing the essential regions are provided for hg19, GRCh37, hs37d5, GRCh38, 
# but a custom bedfile can also be provided in input through the 
# --cnv-somatic-essential-genes-bed=<BEDFILE_PATH> parameter. 
# In such case, the feature is automatically enabled. 
# A custom essential regions bedfile needs to have the following format: 4-column, tab-separated, 
# where the first 3 columns identify the coordinates of the essential region (chromosome, 0-based start, excluded end). 
# The fourth column is the region id (string type). For the purpose of the algorithm, currently only the first 3 columns are used. 
# However, the fourth might be helpful to investigate manually which regions drove the decisions on model plausibility made by the caller.
cnv_somatic_essential_genes_bed: string

# cnv use somatic vc baf (Optional)
# Docs: If running in tumor-normal mode with the SNV caller enabled, use this option
# to specify the germline heterozygous sites.
cnv_use_somatic_vc_baf: false

# cnv use somatic vc vaf (Optional)
# Docs: Use the variant allele frequencies (VAFs) from the somatic SNVs to help select
# the tumor model for the sample.
cnv_use_somatic_vc_vaf: false

# cram input (Optional)
# Docs: Input a normal CRAM file for the variant calling stage
cram_input:
  class: File
  location: icav2://project_id/path/to/file

# cram reference (Optional)
# Docs: Path to the reference fasta file for the CRAM input. 
# Required only if the input is a cram file AND not the reference in the tarball
cram_reference:
  class: File
  location: icav2://project_id/path/to/file

# dbsnp annotation (Optional)
# Docs: In Germline, Tumor-Normal somatic, or Tumor-Only somatic modes,
# DRAGEN can look up variant calls in a dbSNP database and add annotations for any matches that it finds there.
# To enable the dbSNP database search, set the --dbsnp option to the full path to the dbSNP database
# VCF or .vcf.gz file, which must be sorted in reference order.
dbsnp_annotation:
  class: File
  location: icav2://project_id/path/to/file

# deduplicate minimum quality (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual: string

# deduplicate minimum quality germline (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_germline: string

# deduplicate minimum quality somatic (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_somatic: string

# enable cnv calling (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software.
enable_cnv: false

# enable duplicate marking (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking: false

# enable duplicate marking germline (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_germline: false

# enable duplicate marking somatic (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_somatic: false

# enable hla (Optional)
# Docs: Enable HLA typing by setting --enable-hla flag to true
enable_hla: false

# enable hrd (Optional)
# Docs: Set to true to enable HRD scoring to quantify genomic instability.
# Requires somatic CNV calls.
enable_hrd: false

# enable map align (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align: false

# enable map align germline (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align_germline: false

# enable map align output (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output: false

# enable map align output germline (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output_germline: false

# enable map align output somatic (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output_somatic: false

# enable map align somatic (Optional)
# Docs: Enabled by default since --enable-varian...

Assets 10

30 Aug 04:13

github-actions

dragen-alignment-pipeline/4.2.4__20240830041127

93d41dc

dragen-alignment-pipeline/4.2.4__20240830041127

Overview

MD5Sum: 616ac20e7f53bd7d460a83f65e78dc9c

Documentation

Documentation for dragen-alignment-pipeline v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_alignment_pipeline_with_validation_data__4_2_4__20240830041127 / Bundle Version v9_r3__20240830041127

Description
This bundle has been generated by the release of workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-alignment-pipeline/4.2.4__20240830041127.

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

Bundle ID: c8190cc2-4b62-489a-a1a6-433348eccded

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 03689516-b7f8-4dca-bba9-8405b85fae45
Pipeline Code: dragen-alignment-pipeline__4_2_4__20240830041127

Projects

development
staging

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_v39_gencode_annotation
wgs_validation_fastq__cups_pair_8
wgs_validation_fastq__2016_249_17_MH_P033
wgs_validation_fastq__2016_249_18_WH_P025
wgs_validation_fastq__B_ALL_Case_10
wgs_validation_fastq_Diploid_Never_Responder
wgs_validation_fastq_SBJ00303
wgs_validation_fastq_SEQC50
wgs_validation_fastq_SFRC01073
wts_validation_fastq__SBJ00480
wts_validation_fastq__SBJ00028
wts_validation_fastq__SBJ00061
wts_validation_fastq__SBJ00188
wts_validation_fastq__SBJ00199
wts_validation_fastq__SBJ00236
wts_validation_fastq__SBJ00238

Bundle Name: dragen_alignment_pipeline_prod__4_2_4__20240830041127 / Bundle Version v9_r3__20240830041127

Description
This bundle has been generated by the release of workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-alignment-pipeline/4.2.4__20240830041127.

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

Bundle ID: 0a3f1f7a-b497-45b2-b1c5-0d2d507bddd8

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 03689516-b7f8-4dca-bba9-8405b85fae45
Pipeline Code: dragen-alignment-pipeline__4_2_4__20240830041127

Projects

production

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_v39_gencode_annotation

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-alignment-pipeline%2F4.2.4__20240830041127/dragen-alignment-pipeline__4.2.4__20240830041127.schema.json

# aln min score (Optional)
# Docs: (signed) Minimum alignment score to report; baseline for MAPQ.

# When using local alignments (global = 0), aln-min-score is computed by the host software as "22 * match-score".

# When using global alignments (global = 1), aln-min-score is set to -1000000.

# Host software computation may be overridden by setting aln-min-score in configuration file.

# Range: −2,147,483,648 to 2,147,483,647
aln_min_score: string

# alt aware (Optional)
# Docs: Enables special processing for alt contigs, if alt liftover was used in hash table.
# Enabled by default if reference was built with liftover.
alt_aware: false

# ann sj max indel (Optional)
# Docs: Maximum indel length to expect near an annotated splice junction.
# Range: 0 - 63
ann_sj_max_indel: string

# annotation file (Optional)
# Docs: Use to supply a gene annotation file. Required for quantification and gene-fusion.
annotation_file:
  class: File
  location: icav2://project_id/path/to/file

# dedup min qual (Optional)
# Docs: Minimum base quality for calculating read quality metric for deduplication.
# Range: 0-63
dedup_min_qual: string

# edit chain limit (Optional)
# Docs: For edit-mode 1 or 2: Maximum seed chain length in a read to qualify for seed editing.
# Range: > 0
edit_chain_limit: string

# edit mode (Optional)
# Docs: 0 = No edits, 1 = Chain len test, 2 = Paired chain len test, 3 = Edit all std seeds.
edit_mode: '0'

# edit read len (Optional)
# Docs: For edit-mode 1 or 2: Read length in which to try edit-seed-num edited seeds.
# Range: > 0
edit_read_len: string

# edit seed num (Optional)
# Docs: For edit-mode 1 or 2: Requested number of seeds per read to allow editing on.
# Range: > 0
edit_seed_num: string

# en alt hap aln (Optional)
# Docs: Allows chimeric alignments to be output, as supplementary.
en_alt_hap_aln: false

# en chimeric aln (Optional)
# Docs: Allows chimeric alignments to be output, as supplementary.
en_chimeric_aln: false

# enable duplicate marking (Optional)
# Docs: Enable the flagging of duplicate output alignment records.
enable_duplicate_marking: false

# enable map align (Optional)
# Docs: Enable use of BAM input files for mapper/aligner.
enable_map_align: false

# enable map align (Optional)
# Docs: Enables saving the output from the map/align stage.
# If only running map/align, the default value is true.
# If running the variant caller, the default value is false.
# Therefore in the case of the dragen alignment pipeline, this will always be true.
# For sanity purposes, we have it as an option since its default state is not intuitive
enable_map_align_output: false

# enable rna (Optional)
# Docs: Enable rna specific settings
enable_rna: false

# enable rna quantification (Optional)
# Docs: If set to true, enables RNA quantification. Requires --enable-rna to be set to true.
enable_rna_quantification: false

# enable rrna filtering (Optional)
# Docs: Use the DRAGEN RNA pipeline to filter rRNA reads during alignment. The default value is false.
enable_rrna_filter: false

# enable sort (Optional)
# Docs: Enable sorting after mapping/alignment.
enable_sort: false

# fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files for normal sample
# to process (read_1 and read_2 attributes must be presigned urls for each column)
fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# gap ext pen (Optional)
# Docs: Score penalty for gap extension.
gap_ext_pen: string

# gap open pen (Optional)
# Docs: Score penalty for opening a gap (insertion or deletion).
gap_open_pen: string

# generate md tags (Optional)
# Docs: Whether to generate MD tags with alignment output records. Default is false.
generate_md_tags: false

# generate sa tags (Optional)
# Docs: Whether to generate SA:Z tags for records that have chimeric/supplemental alignments.
generate_sa_tags: false

# generate zs tags (Optional)
# Docs: Whether to generate ZS tags for alignment output records. Default is false.
generate_zs_tags: false

# global (Optional)
# Docs: If alignment is global (Needleman-Wunsch) rather than local (Smith-Waterman).
global: false

# hard clips (Optional)
# Docs: Flags for hard clipping: [0] primary, [1] supplementary, [2] secondary.
# The hard-clips option is used as a field of 3 bits, with values ranging from 0 to 7.
# The bits specify alignments, as follows:
#   * Bit 0—primary alignments
#   * Bit 1—supplementary alignments
#   * Bit 2—secondary alignments
# Each bit determines whether local alignments of that type are reported with hard clipping (1)
# or soft clipping (0).
# The default is 6, meaning primary alignments use soft clipping and supplementary and
# secondary alignments use hard clipping.
hard_clips: string

# map orientations (Optional)
# Docs: Constrain orientations to accept forward-only, reverse-complement only, or any alignments.
map_orientations: '0'

# mapq max (Optional)
# Docs: Ceiling on reported MAPQ. Max 255
mapq_max: string

# mapq strict js (Optional)
# Docs: Specific to RNA. When set to 0, a higher MAPQ value is returned, expressing confidence that the alignment is at least partially correct. When set to 1, a lower MAPQ value is returned, expressing the splice junction ambiguity.
mapq_strict_js: false

# match n score (Optional)
# Docs: (signed) Score increment for matching a reference 'N' nucleotide IUB code.
# Range: -16 to 15
match_n_score: string

# match score (Optional)
# Docs: Score increment for matching reference nucleotide.
# When global = 0, match-score > 0; When global = 1, match-score >= 0
match_score: string

# max intron bases (Optional)
# Docs: Maximum intron length reported.
max_intron_bases: string

# max rescues (Optional)
# Docs: Maximum rescue alignments per read pair. Default is 10
max_rescues: string

# min intron bases (Optional)
# Docs: Minimum reference deletion length reported as an intron.
min_intron_bases: string

# min score coeff (Optional)
# Docs: Adjustment to aln-...

Assets 10

20 Aug 08:00

github-actions

umccrise-pipeline/2.3.1--1__20240820075836

fe991b8

umccrise-pipeline/2.3.1--1__20240820075836

Overview

MD5Sum: f2a241d6a5b307335e8ee832532d04f3

Documentation

Documentation for umccrise-pipeline v2.3.1--1

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: umccrise_prod__2_3_1__20240820075836 / Bundle Version v9_r3__20240820075836

Description
This bundle has been generated by the release of workflows/umccrise-pipeline/2.3.1--1/umccrise-pipeline__2.3.1--1.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/umccrise-pipeline/2.3.1--1__20240820075836.

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

Bundle ID: afbb11b1-b3c1-4364-a939-8eecf80b7b74

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 61254f38-b56e-4576-a8a1-341e5c412d11
Pipeline Code: umccrise-pipeline__2_3_1--1__20240820075836

Projects

development
staging
production

Datasets

umccrise_202303

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/umccrise-pipeline%2F2.3.1--1__20240820075836/umccrise-pipeline__2.3.1--1__20240820075836.schema.json

# debug (Optional)
# Docs: Copy workspace to output directory if workflow fails
debug: false

# dragen germline directory (Required)
# Docs: The dragen germline directory
dragen_germline_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# dragen normal id (Optional)
# Docs: The name of the dragen normal sample
dragen_normal_id: string

# dragen somatic directory (Required)
# Docs: The dragen somatic directory
dragen_somatic_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# dragen tumor id (Optional)
# Docs: The name of the dragen tumor sample
dragen_tumor_id: string

# dry run (Optional)
# Docs: Prints rules and commands to be run without actually executing them
dry_run: false

# genomes tar (Required)
# Docs: The reference umccrise tarball
genomes_tar:
  class: File
  location: icav2://project_id/path/to/file

# include stage (Optional)
# Docs: Optionally, specify stage(s) to run
include_stage:
- string

# output directory name (Required)
# Docs: The name of the output directory
output_directory_name: string

# skip stage (Optional)
# Docs: Runs all default stage(s) excluding the one selected
skip_stage:
- string

# subject identifier (Required)
# Docs: The subject ID (used to name output files)
subject_identifier: string

# threads (Optional)
# Docs: Number of threads to use
threads: string

Json

Click to expand!

{
    "debug": false,
    "dragen_germline_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "dragen_normal_id": "string",
    "dragen_somatic_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "dragen_tumor_id": "string",
    "dry_run": false,
    "genomes_tar": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "include_stage": [
        "string"
    ],
    "output_directory_name": "string",
    "skip_stage": [
        "string"
    ],
    "subject_identifier": "string",
    "threads": "string"
}

Outputs Template

Click to expand!

{
    "output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand!

[
    "workflow.cwl#umccrise-pipeline--2.3.1--1/run_umccrise_step"
]

Packed workflow

Click to expand!

[
    "#main/run_umccrise_step"
]

Inputs

Click to expand!

debug

ID: debug

Optional: True
Type: boolean
Docs:
Copy workspace to output directory if workflow fails

dragen germline directory

ID: dragen_germline_directory

Optional: False
Type: Directory
Docs:
The dragen germline directory

dragen normal id

ID: dragen_normal_id

Optional: True
Type: string
Docs:
The name of the dragen normal sample

dragen somatic directory

ID: dragen_somatic_directory

Optional: False
Type: Directory
Docs:
The dragen somatic directory

dragen tumor id

ID: dragen_tumor_id

Optional: True
Type: string
Docs:
The name of the dragen tumor sample

dry run

ID: dry_run

Optional: True
Type: boolean
Docs:
Prints rules and commands to be run without actually executing them

genomes tar

ID: genomes_tar

Optional: False
Type: File
Docs:
The reference umccrise tarball

include stage

ID: include_stage

Optional: True
Type: .[]
Docs:
Optionally, specify stage(s) to run

output directory name

ID: output_directory_name

Optional: False
Type: string
Docs:
The name of the output directory

skip stage

ID: skip_stage

Optional: True
Type: .[]
Docs:
Runs all default stage(s) excluding the one selected

subject identifier

ID: subject_identifier

Optional: False
Type: string
Docs:
The subject ID (used to name output files)

threads

ID: threads

Optional: True
Type: int
Docs:
Number of threads to use

Steps

Click to expand!

run umccrise step

ID: umccrise-pipeline--2.3.1--1/run_umccrise_step

Step Type: tool
Docs:

Run the UMCCRise pipeline

Outputs

Click to expand!

output directory

ID: umccrise-pipeline--2.3.1--1/output_directory

Optional: False
Output Type: Directory
Docs:
The output directory containing the results of the umccrise pipeline

Assets 10

03 Aug 07:48

github-actions

dragen-transcriptome-pipeline/4.2.4__20240803074622

a7d4f5b

dragen-transcriptome-pipeline/4.2.4__20240803074622

Overview

MD5Sum: c142f00004a02ac7d7247c0767ee9ff2

Documentation

Documentation for dragen-transcriptome-pipeline v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_transcriptome_pipeline_with_validation_data__4_2_4__20240803074622 / Bundle Version v9_r3__20240803074622

Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240803074622.

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

Bundle ID: bed469f2-06f0-4f20-a03f-d6ed18dd4ab7

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 66c89437-ec33-4138-8a92-9c018ee533af
Pipeline Code: dragen-transcriptome-pipeline__4_2_4__20240803074622

Projects

development
staging

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_fasta
arriba_2_4_0
hg38_v39_gencode_annotation
wts_validation_fastq__SBJ00480
wts_validation_fastq__SBJ00028
wts_validation_fastq__SBJ00061
wts_validation_fastq__SBJ00188
wts_validation_fastq__SBJ00199
wts_validation_fastq__SBJ00236
wts_validation_fastq__SBJ00238
wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563
wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147
wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620
wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286
wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673

Bundle Name: dragen_transcriptome_pipeline_prod__4_2_4__20240803074622 / Bundle Version v9_r3__20240803074622

Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.2.4/dragen-transcriptome-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.2.4__20240803074622.

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

Bundle ID: b7fa9d82-907d-43f0-9062-ba684d951a5f

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 66c89437-ec33-4138-8a92-9c018ee533af
Pipeline Code: dragen-transcriptome-pipeline__4_2_4__20240803074622

Projects

production

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
hg38_fasta
arriba_2_4_0
hg38_v39_gencode_annotation
wts_multiqc__2023_07_21__4_2_4__Ref_1_Good__SBJ01563
wts_multiqc__2023_07_21__4_2_4__Ref_2_Good__SBJ01147
wts_multiqc__2023_07_21__4_2_4__Ref_3_Good__SBJ01620
wts_multiqc__2023_07_21__4_2_4__Ref_4_Bad__SBJ01286
wts_multiqc__2023_07_21__4_2_4__Ref_5_Bad__SBJ01673

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-transcriptome-pipeline%2F4.2.4__20240803074622/dragen-transcriptome-pipeline__4.2.4__20240803074622.schema.json

# algorithm (Optional)
# Default value: proportional
# Docs: Counting algorithm:
# uniquely-mapped-reads(default) or proportional.
algorithm: "proportional"

# annotation file (Required)
# Docs: Path to annotation transcript file.
annotation_file:
  class: File
  location: icav2://project_id/path/to/file

# bam input (Optional)
# Docs: Input a BAM file for WTS analysis
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# blacklist (Required)
# Docs: File with blacklist range
blacklist:
  class: File
  location: icav2://project_id/path/to/file

# cl config (Optional)
# Docs: command line config to supply additional config values on the command line.
cl_config: string

# contigs (Optional)
# Docs: Optional - List of interesting contigs
# If not specified, defaults to 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
contigs: string

# cytobands (Required)
# Docs: Coordinates of the Giemsa staining bands.
cytobands:
  class: File
  location: icav2://project_id/path/to/file

# enable duplicate marking (Required)
# Docs: Mark identical alignments as duplicates
enable_duplicate_marking: false

# enable map align (Optional)
# Docs: Enabled by default.
# Set this value to false if using bam_input AND tumor_bam_input
enable_map_align: false

# enable map align output (Required)
# Docs: Do you wish to have the output bam files present
enable_map_align_output: false

# enable rna gene fusion (Optional)
# Docs: Optional - Enable the DRAGEN Gene Fusion module - defaults to true
enable_rna_gene_fusion: false

# enable rna quantification (Optional)
# Docs: Optional - Enable the quantification module - defaults to true
enable_rna_quantification: false

# enable sort (Optional)
# Docs: True by default, only set this to false if using --bam-input as input parameter
enable_sort: false

# fastq list (Optional)
# Docs: CSV file that contains a list of FASTQ files
# to process. read_1 and read_2 components in the CSV file must be presigned urls.
fastq_list:
  class: File
  location: icav2://project_id/path/to/file

# Row of fastq lists (Optional)
# Docs: The row of fastq lists.
# Each row has the following attributes:
#   * RGID
#   * RGLB
#   * RGSM
#   * Lane
#   * Read1File
#   * Read2File (optional)
fastq_list_rows:
- rgid: string
  rglb: string
  rgsm: string
  lane: string
  read_1:
    class: File
    location: icav2://project_id/path/to/file
  read_2:
    class: File
    location: icav2://project_id/path/to/file

# java mem (Optional)
# Default value: 20G
# Docs: Set desired Java heap memory size
java_mem: "20G"

# license instance id location (Optional)
# Docs: You may wish to place your own in.
# Optional value, default set to /opt/instance-identity
# which is a path inside the dragen container
lic_instance_id_location:
  class: File
  location: icav2://project_id/path/to/file

# output directory (Required)
# Docs: The directory where all output files are placed
output_directory: string

# output directory name arriba (Optional)
# Default value: arriba
# Docs: Name of the directory to collect arriba outputs in.
output_directory_name_arriba: "arriba"

# output file prefix (Required)
# Docs: The prefix given to all output files
output_file_prefix: string

# protein domains (Required)
# Docs: GFF3 file containing the genomic coordinates of protein domains.
protein_domains:
  class: File
  location: icav2://project_id/path/to/file

# qc reference samples (Required)
# Docs: Reference samples for multiQC report
qc_reference_samples:
- class: Directory
  location: icav2://project_id/path/to/dir/

# read trimming (Optional)
# Docs: To enable trimming filters in hard-trimming mode, set to a comma-separated list of the trimmer tools 
# you would like to use. To disable trimming, set to none. During mapping, artifacts are removed from all reads.
# Read trimming is disabled by default.
read_trimmers: string

# reference Fasta (Required)
# Docs: FastA file with genome sequence
reference_fasta:
  class: File
  location: icav2://project_id/path/to/file

# reference tar (Required)
# Docs: Path to ref data tarball
reference_tar:
  class: File
  location: icav2://project_id/path/to/file

# soft read trimming (Optional)
# Docs: To enable trimming filters in soft-trimming mode, set to a comma-separated list of the trimmer tools 
# you would like to use. To disable soft trimming, set to none. During mapping, reads are aligned as if trimmed,
# and bases are not removed from the reads. Soft-trimming is enabled for the polyg filter by default.
soft_read_trimmers: string

# trim adapter r1 5prime (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 1. 
# NB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.
trim_adapter_r1_5prime:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter read1 (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 1.
trim_adapter_read1:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter read2 (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 3' end of Read 2.
trim_adapter_read2:
  class: File
  location: icav2://project_id/path/to/file

# trim adapter stringency (Optional)
# Docs: Specify the minimum number of adapter bases required for trimming
trim_adapter_stringency: string

# trim adapter r2 5prime (Optional)
# Docs: Specify the FASTA file that contains adapter sequences to trim from the 5' end of Read 2.
# NB: the sequences should be in reverse order (with respect to their appearance in the FASTQ) but not complemented.
trim_dapter_r2_5prime:
  class: File
  location: icav2://project_id/path/to/file

# trim r1 3prime (Optional)
# Docs: Specify the minimum number of bases to trim from the 3' end of Read 1 (default: 0).
trim_r1_3prime: string

# trim r1 5prime (Optional)
# Docs: Specify the minimum number of bases to trim from...

Assets 10

03 Aug 08:02

github-actions

dragen-somatic-with-germline-pipeline/4.2.4__20240803080024

a2a6c8d

dragen-somatic-with-germline-pipeline/4.2.4__20240803080024

Overview

MD5Sum: 2418c871a226483ee9bf79b9cbe66253

Documentation

Documentation for dragen-somatic-with-germline-pipeline
v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_2_4__20240803080024 / Bundle Version v9_r3__20240803080024

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240803080024.

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

Bundle ID: 4d1df713-309a-4bd7-9068-af467dcb7f1c

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: fc82a668-4a60-4acf-a528-38f5ee3ffdf5
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240803080024

Projects

development
staging

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
wgs_validation_fastq__cups_pair_8
wgs_validation_fastq__2016_249_17_MH_P033
wgs_validation_fastq__2016_249_18_WH_P025
wgs_validation_fastq__B_ALL_Case_10
wgs_validation_fastq_Diploid_Never_Responder
wgs_validation_fastq_SBJ00303
wgs_validation_fastq_SEQC50
wgs_validation_fastq_SFRC01073

Bundle Name: dragen_somatic_with_germline_pipeline_prod__4_2_4__20240803080024 / Bundle Version v9_r3__20240803080024

Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.2.4/dragen-somatic-with-germline-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.2.4__20240803080024.

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

Bundle ID: 1a9287d8-9806-4474-a12a-5c08336cbd73

Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: fc82a668-4a60-4acf-a528-38f5ee3ffdf5
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20240803080024

Projects

production

Datasets

dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna

Visual Overview

Click to expand!

Inputs Template

Yaml

Click to expand!

# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-somatic-with-germline-pipeline%2F4.2.4__20240803080024/dragen-somatic-with-germline-pipeline__4.2.4__20240803080024.schema.json

# bam input (Optional)
# Docs: Input a normal BAM file for the variant calling stage
bam_input:
  class: File
  location: icav2://project_id/path/to/file

# cnv enable self normalization (Optional)
# Docs: Enable CNV self normalization.
# Self Normalization requires that the DRAGEN hash table be generated with the enable-cnv=true option.
cnv_enable_self_normalization: false

# cnv normal b allele vcf (Optional)
# Docs: Specify a matched normal SNV VCF.
cnv_normal_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv normal cnv vcf (Optional)
# Docs: Specify germline CNVs from the matched normal sample.
cnv_normal_cnv_vcf: false

# cnv population b allele vcf (Optional)
# Docs: Specify a population SNP catalog.
cnv_population_b_allele_vcf:
  class: File
  location: icav2://project_id/path/to/file

# cnv somatic enable het calling (Optional)
# Docs: Enable HET-calling mode for heterogeneous segments.
cnv_somatic_enable_het_calling: false

# cnv somatic enable lower ploidy limit (Optional)
# Docs: To improve accuracy on the tumor ploidy model estimation, the somatic WGS CNV caller estimates whether the chosen model calls 
# homozygous deletions on regions that are likely to reduce the overall fitness of cells, 
# which are therefore deemed to be "essential" and under negative selection. 
# In the current literature, recent efforts tried to map such cell-essential genes (eg, in 2015 - https://www.science.org/doi/10.1126/science.aac7041).
# The check on essential regions is controlled with --cnv-somatic-enable-lower-ploidy-limit (default true).
cnv_somatic_enable_lower_ploidy_limit: false

# cnv somatic essential genes bed (Optional)
# Docs: Default bedfiles describing the essential regions are provided for hg19, GRCh37, hs37d5, GRCh38, 
# but a custom bedfile can also be provided in input through the 
# --cnv-somatic-essential-genes-bed=<BEDFILE_PATH> parameter. 
# In such case, the feature is automatically enabled. 
# A custom essential regions bedfile needs to have the following format: 4-column, tab-separated, 
# where the first 3 columns identify the coordinates of the essential region (chromosome, 0-based start, excluded end). 
# The fourth column is the region id (string type). For the purpose of the algorithm, currently only the first 3 columns are used. 
# However, the fourth might be helpful to investigate manually which regions drove the decisions on model plausibility made by the caller.
cnv_somatic_essential_genes_bed: string

# cnv use somatic vc baf (Optional)
# Docs: If running in tumor-normal mode with the SNV caller enabled, use this option
# to specify the germline heterozygous sites.
cnv_use_somatic_vc_baf: false

# cnv use somatic vc vaf (Optional)
# Docs: Use the variant allele frequencies (VAFs) from the somatic SNVs to help select
# the tumor model for the sample.
cnv_use_somatic_vc_vaf: false

# cram input (Optional)
# Docs: Input a normal CRAM file for the variant calling stage
cram_input:
  class: File
  location: icav2://project_id/path/to/file

# cram reference (Optional)
# Docs: Path to the reference fasta file for the CRAM input. 
# Required only if the input is a cram file AND not the reference in the tarball
cram_reference:
  class: File
  location: icav2://project_id/path/to/file

# dbsnp annotation (Optional)
# Docs: In Germline, Tumor-Normal somatic, or Tumor-Only somatic modes,
# DRAGEN can look up variant calls in a dbSNP database and add annotations for any matches that it finds there.
# To enable the dbSNP database search, set the --dbsnp option to the full path to the dbSNP database
# VCF or .vcf.gz file, which must be sorted in reference order.
dbsnp_annotation:
  class: File
  location: icav2://project_id/path/to/file

# deduplicate minimum quality (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual: string

# deduplicate minimum quality germline (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_germline: string

# deduplicate minimum quality somatic (Optional)
# Docs: Specifies the Phred quality score below which a base should be excluded from the quality score
# calculation used for choosing among duplicate reads.
dedup_min_qual_somatic: string

# enable cnv calling (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software.
enable_cnv: false

# enable duplicate marking (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking: false

# enable duplicate marking germline (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_germline: false

# enable duplicate marking somatic (Optional)
# Docs: Enable the flagging of duplicate output
# alignment records.
enable_duplicate_marking_somatic: false

# enable hla (Optional)
# Docs: Enable HLA typing by setting --enable-hla flag to true
enable_hla: false

# enable hrd (Optional)
# Docs: Set to true to enable HRD scoring to quantify genomic instability.
# Requires somatic CNV calls.
enable_hrd: false

# enable map align (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align: false

# enable map align germline (Optional)
# Docs: Enabled by default since --enable-variant-caller option is set to true.
# Set this value to false if using bam_input
enable_map_align_germline: false

# enable map align output (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output: false

# enable map align output germline (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output_germline: false

# enable map align output somatic (Optional)
# Docs: Enables saving the output from the
# map/align stage. Default is true when only
# running map/align. Default is false if
# running the variant caller.
enable_map_align_output_somatic: false

# enable map align somatic (Optional)
# Docs: Enabled by default since --enable-varian...

Assets 10

03 Aug 07:48

github-actions

dragen-somatic-with-germline-pipeline/4.2.4__20240803074615

7af9101

dragen-somatic-with-germline-pipeline/4.2.4__20240803074615

Merge pull request #548 from umccr/bugfix/rollback-scratch-space

Qualimap should use scratch directory if it exists, otherwise resort to tmp

Assets 9

Releases: umccr/cwl-ica

dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241030041958

Overview

Documentation

Dockstore

ICAv2

Tenant: umccr-prod

Bundle Name: ora_instrument_run_compression_pipeline_with_reference__4_2_4__20241030041958 / Bundle Version v2__20241030041958

Visual Overview

Inputs Template

Yaml

Json

Outputs Template

Overrides Template

Zipped workflow

Packed workflow

Inputs

instrument run directory

ora check file integrity

ora parallel files

ora print file info

ora reference

ora threads per file

sample id list

Steps

Run Dragen Instrument Run Fastq to ORA

Outputs

output directory

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-wts-qc-pipeline/4.2.4__20240830041140

Overview

Documentation

Dockstore

Visual Overview

Inputs Template

Yaml

Json

Outputs Template

Overrides Template

Zipped workflow

Packed workflow

Inputs

algorithm

annotation file

bam input

enable duplicate marking

enable map align

enable map align output

enable rna gene fusion

enable rna quantification

enable sort

fastq list

Row of fastq lists

java mem

license instance id location

output directory

output file prefix

Bundle Name: ora_instrument_run_compression_pipeline_with_reference__4_2_420241030041958 / Bundle Version v220241030041958

Bundle Name: rnasum_prod__1_1_020240901053225 / Bundle Version 1.1.020240901053225