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_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

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...

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

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...

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...

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-...

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

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...

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...

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

dragen-alignment-pipeline/4.2.4__20240803074610

Overview

MD5Sum: 21c1452ba648cff1cddfbe23a1aa784f

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__20240803074610 / Bundle Version v9_r3__20240803074610

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__20240803074610.

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

Bundle ID: 2fb669db-16ae-49ba-97a4-1b5c4fe376eb

• Bundle Link
  Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
  Pipeline Project Name: pipelines
  Pipeline ID: 413b3c60-a3f5-42eb-a9df-8a77768a8328
  Pipeline Code: dragen-alignment-pipeline__4_2_4__20240803074610

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__20240803074610 / Bundle Version v9_r3__20240803074610

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__20240803074610.

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

Bundle ID: 67140b8d-df64-4878-931c-7b52aa15d6cb

• Bundle Link
  Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
  Pipeline Project Name: pipelines
  Pipeline ID: 413b3c60-a3f5-42eb-a9df-8a77768a8328
  Pipeline Code: dragen-alignment-pipeline__4_2_4__20240803074610

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__20240803074610/dragen-alignment-pipeline__4.2.4__20240803074610.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-...