Releases: umccr/cwl-ica
Releases · umccr/cwl-ica
dragen-somatic-with-germline-pipeline/4.3.6__20241115073817
Overview
MD5Sum: 34be195a66bd929ae3ba18b0c7ec10a8
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.3.6
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_3_6__20241115073817 / Bundle Version v10_r4__20241115073817
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241115073817.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: aef12d8c-055e-4a5c-a949-7200d296e3aa
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: adeb223a-0a84-43bc-a13a-9bf0ed31e565
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241115073817
Projects
- development
- staging
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- 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_3_6__20241115073817 / Bundle Version v10_r4__20241115073817
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241115073817.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: dee75735-a97c-4572-b51e-04776a4fdc36
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: adeb223a-0a84-43bc-a13a-9bf0ed31e565
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241115073817
Projects
- production
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
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%2F4.3.6__20241115073817/dragen-somatic-with-germline-pipeline__4.3.6__20241115073817.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 cnv germline (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (somatic only)
enable_cnv_germline: false
# enable cnv somatic (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (germline only)
enable_cnv_somatic: 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....
dragen-somatic-with-germline-pipeline/4.3.6__20241115045341
Overview
MD5Sum: 76caa14272dd68d3a994738b73dcb7d7
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.3.6
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_3_6__20241115045341 / Bundle Version v10_r4__20241115045341
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241115045341.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: 8a354985-78c6-4fc8-90ed-00b92dde5091
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 3c5ea2c7-dedf-4f3e-92ee-ca66a619ad39
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241115045341
Projects
- development
- staging
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- 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_3_6__20241115045341 / Bundle Version v10_r4__20241115045341
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241115045341.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: ceb34a28-344c-4fd7-808b-881468e91ded
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 3c5ea2c7-dedf-4f3e-92ee-ca66a619ad39
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241115045341
Projects
- production
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
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%2F4.3.6__20241115045341/dragen-somatic-with-germline-pipeline__4.3.6__20241115045341.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 cnv germline (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (somatic only)
enable_cnv_germline: false
# enable cnv somatic (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (germline only)
enable_cnv_somatic: 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....
dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241115064819
Overview
MD5Sum: d292da07e5425d9879ba869ab58ff316
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__20241115064819 / Bundle Version v2__20241115064819
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__20241115064819.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v2
Bundle ID: 0525e2ef-1cc5-4821-a6c2-e5240d5b82c1
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 38728164-d932-431e-a015-80c019f814f2
Pipeline Code: dragen-instrument-run-fastq-to-ora-pipeline__4_2_4__20241115064819
Projects
- development
- staging
- production
Datasets
- ora_reference_v2
Visual Overview
Click to expand!
Inputs Template
Yaml
Click to expand!
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-instrument-run-fastq-to-ora-pipeline%2F4.2.4__20241115064819/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241115064819.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
dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241115044412
Overview
MD5Sum: 9df445c3fdd3b101f1061ae0a29d7fa0
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__20241115044412 / Bundle Version v2__20241115044412
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__20241115044412.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v2
Bundle ID: 9fb2017a-bb15-4551-8209-a41e436bf808
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 456a1e54-acc7-44bd-a516-b1eb4e91e955
Pipeline Code: dragen-instrument-run-fastq-to-ora-pipeline__4_2_4__20241115044412
Projects
- development
- staging
- production
Datasets
- ora_reference_v2
Visual Overview
Click to expand!
Inputs Template
Yaml
Click to expand!
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-instrument-run-fastq-to-ora-pipeline%2F4.2.4__20241115044412/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241115044412.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
dragen-somatic-with-germline-pipeline/4.2.4__20241114110541
Overview
MD5Sum: a4bb1e0adbb53a10308b11c87cfe2f27
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__20241114110541 / Bundle Version v9_r3__20241114110541
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__20241114110541.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3
Bundle ID: bf46d893-2084-4cf9-bd34-363790bfa827
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 988af91b-d707-49ed-9107-8994f75cef12
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20241114110541
Projects
- development
- staging
Datasets
- dragen_hash_table_hg38_alt_masked_v9_r3_linear_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
- ora_reference_v2
Bundle Name: dragen_somatic_with_germline_pipeline_prod__4_2_4__20241114110541 / Bundle Version v9_r3__20241114110541
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__20241114110541.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3
Bundle ID: f37b2451-f65a-4127-9f5d-29b5c9433a8d
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 988af91b-d707-49ed-9107-8994f75cef12
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20241114110541
Projects
- production
Datasets
- dragen_hash_table_hg38_alt_masked_v9_r3_linear_cnv_hla_rna
- ora_reference_v2
Visual Overview
Click to expand!
Inputs Template
Yaml
Click to expand!
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-somatic-with-germline-pipeline%2F4.2.4__20241114110541/dragen-somatic-with-germline-pipeline__4.2.4__20241114110541.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 cnv germline (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (somatic only)
enable_cnv_germline: false
# enable cnv somatic (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (germline only)
enable_cnv_somatic: 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
#...
rnasum-pipeline/1.1.5__20241112044604
Overview
MD5Sum: 7fec44c37ab6d7f991a40c3a02925e6a
Documentation
Documentation for rnasum-pipeline v1.1.5
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: rnasum_prod__1_1_5__20241112044604 / Bundle Version 1.0.0__20241112044604
Description
This bundle has been generated by the release of workflows/rnasum-pipeline/1.1.5/rnasum-pipeline__1.1.5.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/rnasum-pipeline/1.1.5__20241112044604.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is 1.0.0
Bundle ID: 83a8ff6f-405a-4068-b22d-a22e1cad63e3
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: c412a2ee-5a92-465d-b619-7516da56b9bf
Pipeline Code: rnasum-pipeline__1_1_5__20241112044604
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%2F1.1.5__20241112044604/rnasum-pipeline__1.1.5__20241112044604.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
# 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
# structural variants tsv (Optional)
# Docs: Location of the tsv output from SV caller
sv_tsv:
class: File
location: icav2://project_id/path/to/file
# 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,
"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",
"sv_tsv": {
"class": "File",
"location": "icav2://project_id/path/to/file"
},
"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--1.1.5/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: dat...
dragen-somatic-with-germline-pipeline/4.3.6__20241107061820
Overview
MD5Sum: f6f250deff3ce3eb74c05da342e970ea
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.3.6
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_3_6__20241107061820 / Bundle Version v10_r4__20241107061820
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241107061820.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: 0ae597fa-eec3-43a0-9674-5c36a79d0cf3
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: a2332db7-caa3-4eb9-81c9-e32a36c94953
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241107061820
Projects
- development
- staging
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- 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_3_6__20241107061820 / Bundle Version v10_r4__20241107061820
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241107061820.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: 924f5fa1-7bdd-417d-8ab1-a47d615ae396
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: a2332db7-caa3-4eb9-81c9-e32a36c94953
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241107061820
Projects
- production
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
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%2F4.3.6__20241107061820/dragen-somatic-with-germline-pipeline__4.3.6__20241107061820.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 cnv germline (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (somatic only)
enable_cnv_germline: false
# enable cnv somatic (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (germline only)
enable_cnv_somatic: 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....
dragen-somatic-with-germline-pipeline/4.2.4__20241107061831
Overview
MD5Sum: 8bcca124af5ca64c963a42da1b9d985f
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__20241107061831 / Bundle Version v9_r3__20241107061831
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__20241107061831.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3
Bundle ID: 96e6b046-6ad1-4148-bcb0-d195f362ce60
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 6ce2b636-ba2f-4004-8065-f3557f286c98
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20241107061831
Projects
- development
- staging
Datasets
- dragen_hash_table_hg38_alt_masked_v9_r3_linear_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__20241107061831 / Bundle Version v9_r3__20241107061831
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__20241107061831.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3
Bundle ID: 67fd8601-f442-4592-88cc-d99dbd3b1f4d
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 6ce2b636-ba2f-4004-8065-f3557f286c98
Pipeline Code: dragen-somatic-with-germline-pipeline__4_2_4__20241107061831
Projects
- production
Datasets
- dragen_hash_table_hg38_alt_masked_v9_r3_linear_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__20241107061831/dragen-somatic-with-germline-pipeline__4.2.4__20241107061831.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 cnv germline (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (somatic only)
enable_cnv_germline: false
# enable cnv somatic (Optional)
# Docs: Enable CNV processing in the DRAGEN Host Software (germline only)
enable_cnv_somatic: 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 (Opti...
dragen-transcriptome-pipeline/4.3.6__20241106102659
Overview
MD5Sum: c9e823dbdf406f61e221a4eee400a8f4
Documentation
Documentation for dragen-transcriptome-pipeline v4.3.6
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: dragen_transcriptome_pipeline_with_validation_data__4_3_6__20241106102659 / Bundle Version v10_r4__20241106102659
Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.3.6/dragen-transcriptome-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.3.6__20241106102659.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: f23b0978-e6d5-44da-b601-398fcc0660d6
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: c309cddb-bb49-4f96-926e-6917ef0b18d6
Pipeline Code: dragen-transcriptome-pipeline__4_3_6__20241106102659
Projects
- development
- staging
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- 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
Bundle Name: dragen_transcriptome_pipeline_prod__4_3_6__20241106102659 / Bundle Version v10_r4__20241106102659
Description
This bundle has been generated by the release of workflows/dragen-transcriptome-pipeline/4.3.6/dragen-transcriptome-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-transcriptome-pipeline/4.3.6__20241106102659.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: b5da4efb-449f-4277-bfdd-35251eaac849
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: c309cddb-bb49-4f96-926e-6917ef0b18d6
Pipeline Code: dragen-transcriptome-pipeline__4_3_6__20241106102659
Projects
- production
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- hg38_fasta
- arriba_2_4_0
- hg38_v39_gencode_annotation
Visual Overview
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Inputs Template
Yaml
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# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-transcriptome-pipeline%2F4.3.6__20241106102659/dragen-transcriptome-pipeline__4.3.6__20241106102659.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
# 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 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_adapter_r2_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 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 from the 5' end of Read 2 (default: 0).
trim_r2_5prime: string
Json
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{
"algorithm": "proportional",
"annotation_file": {
"class": "File",
"location": "icav2...
dragen-somatic-with-germline-pipeline/4.3.6__20241106102705
Overview
MD5Sum: 9585b66b4fb95e312c4a76e47d4697b1
Documentation
Documentation for dragen-somatic-with-germline-pipeline
v4.3.6
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: dragen_somatic_with_germline_pipeline_with_validation_data__4_3_6__20241106102705 / Bundle Version v10_r4__20241106102705
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241106102705.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: 84321a34-a7be-41ea-9e71-148b6f92b2c9
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 4dd83fe0-1119-4dfc-8600-98f524cefe5e
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241106102705
Projects
- development
- staging
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
- 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_3_6__20241106102705 / Bundle Version v10_r4__20241106102705
Description
This bundle has been generated by the release of workflows/dragen-somatic-with-germline-pipeline/4.3.6/dragen-somatic-with-germline-pipeline__4.3.6.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-somatic-with-germline-pipeline/4.3.6__20241106102705.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v10_r4
Bundle ID: 1511947c-e511-42b5-8eb3-6f061caccc20
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: 4dd83fe0-1119-4dfc-8600-98f524cefe5e
Pipeline Code: dragen-somatic-with-germline-pipeline__4_3_6__20241106102705
Projects
- production
Datasets
- dragen_hash_table_chm13_v2_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_chm13_v2_v10_r4_linear_cnv_hla_rna_methylated_combined
- dragen_hash_table_hg38_alt_masked_v10_r4_graph_cnv_hla_rna
- dragen_hash_table_hg38_alt_masked_v10_r4_linear_cnv_hla_rna_methylated_combined
Visual Overview
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Inputs Template
Yaml
Click to expand!
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-somatic-with-germline-pipeline%2F4.3.6__20241106102705/dragen-somatic-with-germline-pipeline__4.3.6__20241106102705.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
# r...