Releases: umccr/cwl-ica
dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241030041958
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
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: ora_instrument_run_compression_pipeline_with_reference__4_2_4__20241030041958 / Bundle Version v2__20241030041958
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
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
rnasum-pipeline/1.1.0__20240901053225
Overview
MD5Sum: 28bb78f3359e7f977c4be97880886a02
Documentation
Documentation for rnasum-pipeline v1.1.0
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: rnasum_prod__1_1_0__20240901053225 / Bundle Version 1.1.0__20240901053225
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
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...
dragen-wts-qc-pipeline/4.2.4__20240830041140
Overview
MD5Sum: 734930b3b2ef27e53799d54e9c47e37d
Documentation
Documentation for dragen-wts-qc-pipeline v4.2.4
Dockstore
Visual Overview
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
dragen-transcriptome-pipeline/4.2.4__20240830041834
Overview
MD5Sum: d8bbfbee2f713b2ea768d5ea8a8285b9
Documentation
Documentation for dragen-transcriptome-pipeline v4.2.4
Dockstore
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
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...
dragen-somatic-with-germline-pipeline/4.2.4__20240830041201
Overview
MD5Sum: a9d59f7474a1b87d531c2a859a29316d
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.2.4
Dockstore
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
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...
dragen-alignment-pipeline/4.2.4__20240830041127
Overview
MD5Sum: 616ac20e7f53bd7d460a83f65e78dc9c
Documentation
Documentation for dragen-alignment-pipeline v4.2.4
Dockstore
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
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-...
umccrise-pipeline/2.3.1--1__20240820075836
Overview
MD5Sum: f2a241d6a5b307335e8ee832532d04f3
Documentation
Documentation for umccrise-pipeline v2.3.1--1
Dockstore
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
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
dragen-transcriptome-pipeline/4.2.4__20240803074622
Overview
MD5Sum: c142f00004a02ac7d7247c0767ee9ff2
Documentation
Documentation for dragen-transcriptome-pipeline v4.2.4
Dockstore
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
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...
dragen-somatic-with-germline-pipeline/4.2.4__20240803080024
Overview
MD5Sum: 2418c871a226483ee9bf79b9cbe66253
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.2.4
Dockstore
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
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...
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