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dragen-wgts-dna-pipeline/4.4.4__20250915021010

15 Sep 02:12
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Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250915021010 / Bundle Version v11_r5__20250915021010

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250915021010.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: d9b195be-1352-4e42-a7f3-aeb2217efa32

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: defdcf63-27c9-4e7b-9b5d-f621376c1f59
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250915021010

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250915021010 / Bundle Version v11_r5__20250915021010

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250915021010.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 5fc299de-4518-46f7-9f06-2179eef91c7e

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: defdcf63-27c9-4e7b-9b5d-f621376c1f59
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250915021010

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250915021010/dragen-wgts-dna-pipeline__4.4.4__20250915021010.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250902012720

02 Sep 01:29
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250902012720
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dragen-wgts-dna-pipeline/4.4.4__20250902012720

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250902012720 / Bundle Version v11_r5__20250902012720

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250902012720.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: be50ca0c-1099-416a-8a65-d44d68188a55

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 0c7b15f1-f5d4-433a-9333-4618e5ca1731
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250902012720

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250902012720 / Bundle Version v11_r5__20250902012720

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250902012720.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 9728cd22-f150-4a38-8cf3-e16c41f56549

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 0c7b15f1-f5d4-433a-9333-4618e5ca1731
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250902012720

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250902012720/dragen-wgts-dna-pipeline__4.4.4__20250902012720.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
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dragen-wgts-dna-pipeline/4.4.4__20250901220047

01 Sep 22:02
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250901220047
0a9862c
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dragen-wgts-dna-pipeline/4.4.4__20250901220047

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250901220047 / Bundle Version v11_r5__20250901220047

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250901220047.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: c5df5fcc-49e7-4493-8bd7-a5f71ccf924a

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: d83b1056-57a9-499a-b0ef-834f6e2cb229
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250901220047

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250901220047 / Bundle Version v11_r5__20250901220047

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250901220047.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: e85e1d34-b695-4086-a42c-a761e70983bd

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: d83b1056-57a9-499a-b0ef-834f6e2cb229
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250901220047

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250901220047/dragen-wgts-dna-pipeline__4.4.4__20250901220047.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250901010327

01 Sep 01:05
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250901010327
b070f41
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dragen-wgts-dna-pipeline/4.4.4__20250901010327

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250901010327 / Bundle Version v11_r5__20250901010327

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250901010327.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: b5d32b66-83b9-45ef-8978-b222eb658f2e

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: e436c569-6022-4dfb-9692-3f265522a66f
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250901010327

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250901010327 / Bundle Version v11_r5__20250901010327

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250901010327.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: fa4bb886-5020-46c1-8e2c-8a3e511708ec

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: e436c569-6022-4dfb-9692-3f265522a66f
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250901010327

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250901010327/dragen-wgts-dna-pipeline__4.4.4__20250901010327.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250831041955

31 Aug 04:21
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250831041955
a832917
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Choose a tag to compare
dragen-wgts-dna-pipeline/4.4.4__20250831041955

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250831041955 / Bundle Version v11_r5__20250831041955

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250831041955.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 4b54316c-9698-4107-bfcc-5d5aeb587417

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: c8a273d6-bd83-44de-b2b7-3df53d21b278
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250831041955

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250831041955 / Bundle Version v11_r5__20250831041955

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250831041955.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 00161db3-3123-4c6e-b620-843968b444d3

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: c8a273d6-bd83-44de-b2b7-3df53d21b278
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250831041955

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250831041955/dragen-wgts-dna-pipeline__4.4.4__20250831041955.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
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dragen-wgts-dna-pipeline/4.4.4__20250827053004

27 Aug 05:31
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dragen-wgts-dna-pipeline/4.4.4__20250827053004
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dragen-wgts-dna-pipeline/4.4.4__20250827053004

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250827053004 / Bundle Version v11_r5__20250827053004

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250827053004.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 3f0c7127-8aef-4a1b-ba4f-b9c1a77a6fe3

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 6868123f-a845-444f-a32f-5cda8c56302b
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250827053004

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250827053004 / Bundle Version v11_r5__20250827053004

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250827053004.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 011e4bb7-04f3-47c3-ae8a-92a19379cb31

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 6868123f-a845-444f-a32f-5cda8c56302b
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250827053004

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250827053004/dragen-wgts-dna-pipeline__4.4.4__20250827053004.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
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dragen-wgts-rna-pipeline/4.4.4__20250822040654

22 Aug 04:10
@github-actions github-actions
dragen-wgts-rna-pipeline/4.4.4__20250822040654
20d534e
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dragen-wgts-rna-pipeline/4.4.4__20250822040654

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-rna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file, reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • Run the dragen rna pipeline
  • Run multiqc on the outputs of the dragen rna pipeline

Inputs:
This pipeline differs from our previous rna pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-rna pipelines
The outputs are:
* Dragen rna output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

Visual Overview

Click to expand!

dragen-wgts-rna-pipeline

Subworkflows

dragen-wgts-rna-variant-calling-stage__4.4.4.cwl

dragen-wgts-rna-variant-calling-stage__4.4.4.cwl

dragen-create-aligner-options-object__4.4.4.cwl

dragen-create-aligner-options-object__4.4.4.cwl

dragen-create-wgts-rna-variant-calling-options-object__4.4.4.cwl

dragen-create-wgts-rna-variant-calling-options-object__4.4.4.cwl

dragen-create-wgts-alignment-options-object__4.4.4.cwl

dragen-create-wgts-alignment-options-object__4.4.4.cwl

dragen-create-mapper-options-object__4.4.4.cwl

dragen-create-mapper-options-object__4.4.4.cwl

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-wgts-rna-pipeline%2F4.4.4__20250822040654/dragen-wgts-rna-pipeline__4.4.4__20250822040654.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# annotation file (Optional)
# Docs: The annotation file to be used for
# gene expression quantification, splice variant calling, and gene fusion calling
annotation_file:
  class: File
  location: icav2://project_id/path/to/file

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# snv variant calling options (Optional)
# Docs: The options to be used for rna variant calling.
# This is a JSON object that contains the options to be used for variant calling.
# This is passed to the Dragen variant calling tool.
snv_variant_caller_options:
  enable_variant_caller: false
  enable_methylation_calling: false
  enable_variant_deduplication: false
  enable_vcf_compression: false
  enable_vcf_indexing: false
  dbsnp:
    class: File
    location: icav2://project_id/path/to/file
  vd_eh_vcf:
    class: File
    location: icav2://project_id/path/to/file
  vd_output_match_log: false
  vd_small_variant_vcf:
    class: File
    location: icav2://project_id/path/to/file
  vd_sv_vcf:
    class: File
    location: icav2://project_id/path/to/file
  dn_cnv_vcf:
    class: File
    location: icav2://project_id/path/to/file
  dn_input_vcf:
    class: File
    location: icav2://project_id/path/to/file
  dn_output_vcf:
    class: File
    location: icav2://project_id/path/to/file
  dn_sv_vcf:
    class: File
    location: icav2://project_id/path/to/file
  enable_joint_genotyping: false
  enable_multi_sample_gvcf: false
  enable_vlrd: false
  pedigree_file:
    class: File
    location: icav2://project_id/path/to/file
  qc_snp_denovo_quality_threshold: string
  qc_indel_denovo_quality_threshold: string
  variant:
    class: File
    location: icav2://project_id/path/to/file
  variant_list:
    class: File
    location: icav2://project_id/path/to/file
  vc_af_call_threshold: string
  vc_af_filter_threshold: string
  vc_af_call_threshold_mito: string
  vc_af_filter_threshold_mito: string
  vc_callability_normal_threshold: string
  vc_callability_tumor_threshold: string
  vc_clustered_event_penalty: string
  vc_decoy_contigs:
  vc_depth_annotation_threshold: string
  vc_depth_filter_threshold: string
  vc_emit_ref_confidence: string
  rna_vc_enable_homozygous_genotype: false
  rna_vc_homozygous_genotype_af_threshold:
  vc_max_alternate_alleles: string
  vc_emit_zero_coverage_intervals: false
  vc_mnv_emit_component_calls: false
  vc_combine_phased_variants_distance: string
  vc_combine_phased_variants_max_vaf_delta:
  vc_combine_phased_variants_distance_snvs_only: string
  qc_detect_contamination: false

# gene fusion detection options (Optional)
# Docs: The Gene Fusion Detection options for the rna gene fusion detection
gene_fusion_detection_options:
  enable_rna_gene_fusion: false
  rna_gf_blast_pairs:
    class: File
    location: icav2://project_id/path/to/file

# gene expression quantification options (Optional)
# Docs: The Gene Expression Quantification options for the rna gene expression quantification
gene_expression_quantification_options:
  enable_rna_quantification: false
  rna_quantification_gc_bias: false
  rna_quantification_fld_max: string
  rna_quantification_fld_mean: string
  rna_quantification_fld_sd: string
  rna_quantification_tlen_min: string

# splice variant caller options (Optional)
# Docs: The Splice Variant Caller options for the rna spl...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250822104303

22 Aug 10:44
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dragen-wgts-dna-pipeline/4.4.4__20250822104303

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250822104303 / Bundle Version v11_r5__20250822104303

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250822104303.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 54473d95-84e8-400d-9a1c-86782aec21e1

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: f6a4c255-5d49-4379-91ec-dd89b76a213f
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250822104303

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250822104303 / Bundle Version v11_r5__20250822104303

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250822104303.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: a063caa0-5b7a-480f-85e0-1a39ff7ad98e

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: f6a4c255-5d49-4379-91ec-dd89b76a213f
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250822104303

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250822104303/dragen-wgts-dna-pipeline__4.4.4__20250822104303.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250822034548

22 Aug 03:47
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250822034548
63c016e
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dragen-wgts-dna-pipeline/4.4.4__20250822034548

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250822034548 / Bundle Version v11_r5__20250822034548

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250822034548.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 6abf113b-27dd-46ad-91c9-8e59364ca599

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 1ce7dab7-6f83-48c6-8a06-173d06048504
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250822034548

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250822034548 / Bundle Version v11_r5__20250822034548

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250822034548.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 416025c3-7cca-49c0-8be4-d42a0cd0abd3

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 1ce7dab7-6f83-48c6-8a06-173d06048504
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250822034548

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250822034548/dragen-wgts-dna-pipeline__4.4.4__20250822034548.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
Read more
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dragen-wgts-dna-pipeline/4.4.4__20250805055151

05 Aug 05:53
@github-actions github-actions
dragen-wgts-dna-pipeline/4.4.4__20250805055151
2b0b297
Compare
Choose a tag to compare
dragen-wgts-dna-pipeline/4.4.4__20250805055151

Overview

MD5Sum: None

Documentation

Dragen dragen-wgts-dna-pipeline v4.4.4

Performs the following steps:

  • If input is a bam file (for tumor or normal), reheader the bam file such that the rgsm value matches
    the output_prefix value. We can't do this inside the dragen container since it doesn't have the samtools binary installed.
    Instead we run a seperate step to reheader the bam file.
  • If tumor sequence data is provided and normal sequence data are provided, run the dragen-somatic tool.
  • If only the normal sequence data are provided, run the dragen-germline tool.

Inputs:
This pipeline differs from our previous dragen-germline and dragen-somatic pipeline by instead grouping inputs.
This makes overall workflow cwl file much smaller, and the workflow graphs much more readable.
It also means appending input options is much easier since it involves updating just one schema yaml file,
rather than the workflow inputs, workflow steps and the tool inputs.
Most of the grunt work is done in the dragen tools typescript file to convert input options into a configuration file.

Outputs:
The outputs are the same as the previous dragen-germline and dragen-somatic pipelines.
The outputs are:
* Dragen somatic output directory (if tumor sequence data are provided)
* Dragen germline output directory (always)
* Multiqc output directory (always)

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_wgts_dna_pipeline_with_validation_data_v4_4_4__20250805055151 / Bundle Version v11_r5__20250805055151

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250805055151.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: 57c39c53-7c3f-4713-8f3e-b721adf9712a

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 3dff2d05-569a-4b5a-88b8-bdca48a121bd
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250805055151

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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_wgts_dna_pipeline_production_v4_4_4__20250805055151 / Bundle Version v11_r5__20250805055151

Description
This bundle has been generated by the release of workflows/dragen-wgts-dna-pipeline/4.4.4/dragen-wgts-dna-pipeline__4.4.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-wgts-dna-pipeline/4.4.4__20250805055151.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v11_r5

Bundle ID: ab287c5d-5222-40a9-bf61-64660c54585f

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 3dff2d05-569a-4b5a-88b8-bdca48a121bd
    Pipeline Code: dragen-wgts-dna-pipeline__4_4_4__20250805055151

Projects

  • production

Datasets

  • dragen_hash_table_chm13_v2_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_chm13_v2_v11_r5_graph_cnv_hla_methyl_cg_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_linear_cnv_hla_methyl_cg_methylated_combined_rna
  • dragen_hash_table_hg38_alt_masked_v11_r5_graph_cnv_hla_methyl_cg_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-wgts-dna-pipeline%2F4.4.4__20250805055151/dragen-wgts-dna-pipeline__4.4.4__20250805055151.schema.json

# sequence data (Required)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# tumor sequence data (Optional)
# Docs: The sequence data to be aligned and called variants on.
# This can either be a bam file, cram file or a list of fastq list row objects
# Only specify the tumor sequence data IF you want to run the somatic variant calling pipeline.
tumor_sequence_data:
  fastq_list_rows:
    rgid: string
    rglb: string
    rgsm: string
    rgcn: string
    rgds: string
    rgdt: string
    rgpl: 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

# reference (Required)
# Docs: The reference genome to be used for alignment and variant calling.
reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# somatic reference (Optional)
# Docs: The somatic reference genome to be used for alignment and variant calling.
# This is only used if the somatic reference is different from the normal reference.
somatic_reference:
  name: string
  structure:
  tarball:
    class: File
    location: icav2://project_id/path/to/file

# reference (Optional)
# Docs: The ora reference used to decompress the input fastq files,
# required if any of the fastqs are ora-compressed
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# sample name (Required)
# Docs: The sample name to be used for alignment and variant calling.
# This is used to name the output files
sample_name: string

# tumor sample name (Optional)
# Docs: The tumor sample name to be used for alignment and variant calling.
# This is used to name the output files
tumor_sample_name: string

# alignment options (Optional)
# Docs: The options to be used for alignment.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: false
  input_qname_suffix_delimiter: string
  output_format: string
  preserve_bqsr_tags: false
  preserve_map_align_order: false
  qc_coverage:
    region:
      class: File
      location: icav2://project_id/path/to/file
    report_type: string
    thresholds:
    - string
  ref_sequence_filter: false
  remove_duplicates: false
  sample_size: string
  strip_input_qname_suffixes: false
  aligner:
    aln_min_score: string
    clip_pe_overhang: string
    dedup_min_qual: string
    en_alt_hap_aln: string
    en_chimeric_aln: string
    gap_ext_pen: string
    gap_open_pen: string
    global: string
    hard_clip_tags: string
    hard_clips: string
    mapq_floor_1snp: string
    map_orientations: string
    mapq_max: string
    mapq_strict_sjs: string
    match_n_score: string
    match_score: string
    max_rescues: string
    min_overhang: string
    min_score_coeff:
    mismatch_pen: string
    no_noncan_motifs: string
    no_unclip_score: string
    no_unpaired: string
    pe_max_penalty: string
    pe_orientation: string
    rescue_sigmas:
    sec_aligns: string
    sec_aligns_hard: string
    sec_phred_delta: string
    sec_score_delta:
    supp_aligns: string
    supp_as_sec: string
    supp_min_score_adj: string
    unclip_score: string
    unpaired_pen: string
  mapper:
    ann_sj_max_indel: string
    edit_chain_limit: string
    edit_mode: string
    edit_read_len: string
    edit_seed_num: string
    map_orientations: string
    max_intron_bases: string
    min_intron_bases: string
    seed_density: string
  rrna_filter_enable: false
  rrna_filter_contig: string
  rna_library_type: string
  rna_mapq_unique: string
  rna_ann_sj_min_len: string

# somatic alignment options (Optional)
# Docs: The options to be used for alignment of the tumor sample.
# This is a JSON object that contains the options to be used for alignment.
# This is passed to the Dragen alignment tool.
# For the somatic alignment, both alignment options and somatic alignment options are first merged before being provided to dragen
somatic_alignment_options:
  enable_duplicate_marking: false
  enable_deterministic_sort: false
  enable_sampling: false
  enable_down_sampler: false
  append_read_index_to_name: false
  fastq_offset: string
  filter_flags_from_output: string
  generate_md_tags: false
  generate_sa_tags: false
  generate_zs_tags: fals...
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