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dragen-alignment-pipeline/4.2.4__20240627051848

27 Jun 05:20
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dragen-alignment-pipeline/4.2.4__20240627051848

Overview

MD5Sum: 87e2a6e6000fed3dd32e2de6f0639240

Documentation

Documentation for dragen-alignment-pipeline v4.2.4

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: dragen_alignment_pipeline_with_validation_data__4_2_4__20240627051848 / Bundle Version v9_r3__20240627051848

Description
This bundle has been generated by the release of workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-alignment-pipeline/4.2.4__20240627051848.

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

Bundle ID: 507adadf-f046-4547-acfb-2c7773ab04cf

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: fcc6d555-4ea3-414e-8264-3bf362d81c58
    Pipeline Code: dragen-alignment-pipeline__4_2_4__20240627051848

Projects

  • development
  • staging

Datasets

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

Bundle Name: dragen_alignment_pipeline_prod__4_2_4__20240627051848 / Bundle Version v9_r3__20240627051848

Description
This bundle has been generated by the release of workflows/dragen-alignment-pipeline/4.2.4/dragen-alignment-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-alignment-pipeline/4.2.4__20240627051848.

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

Bundle ID: fdc59e54-d067-440a-97c8-0d28ff19cef3

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: fcc6d555-4ea3-414e-8264-3bf362d81c58
    Pipeline Code: dragen-alignment-pipeline__4_2_4__20240627051848

Projects

  • production

Datasets

  • dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna

Visual Overview

Click to expand!

dragen-alignment-pipeline

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-alignment-pipeline%2F4.2.4__20240627051848/dragen-alignment-pipeline__4.2.4__20240627051848.schema.json

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

# min score coeff (Optional)
# Docs: Adjustment to aln-min-score per read base.
# Range: -64 to 63.999
min_score_co...
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Assets 10
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bclconvert-interop-qc/1.3.1--1.21__20240627051309

27 Jun 05:14
@github-actions github-actions
bclconvert-interop-qc/1.3.1--1.21__20240627051309
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bclconvert-interop-qc/1.3.1--1.21__20240627051309

Overview

MD5Sum: ac758f18a4438440d8c1cae45eb5ffb1

Documentation

Documentation for bclconvert-interop-qc v1.3.1--1.21
This workflow has been designed for BCLConvert 4.2.7 outputs from the Nextflow autolaunch pipeline.
The InterOp directory is expected to contain the IndexMetricsOut.bin file, otherwise the
index summary will not be generated.
It is assumed that the Reports directory will contain the RunInfo.xml file

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: bclconvert_interop_qc_prod__1_3_1__1_21__20240627051309 / Bundle Version 1.3.1__1.21__20240627051309

Description
This bundle has been generated by the release of workflows/bclconvert-interop-qc/1.3.1--1.21/bclconvert-interop-qc__1.3.1--1.21.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/bclconvert-interop-qc/1.3.1--1.21__20240627051309.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is 1.3.1__1.21

Bundle ID: 7f394774-6ff4-4d0a-b453-6cf64d2c7c07

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 35cae57c-8895-4814-ae89-db4b5e9668b2
    Pipeline Code: bclconvert-interop-qc__1_3_1--1_21__20240627051309

Projects

  • development
  • staging
  • production

Visual Overview

Click to expand!

bclconvert-interop-qc

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/bclconvert-interop-qc%2F1.3.1--1.21__20240627051309/bclconvert-interop-qc__1.3.1--1.21__20240627051309.schema.json

# BCLConvert Report Directory (Required)
# Docs: The output directory from a BCLConvert run named 'Reports'
bclconvert_report_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# Instrument Run ID (Required)
# Docs: The instrument run ID
instrument_run_id: string

# Interop Directory (Required)
# Docs: The interop directory
interop_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

Json

Click to expand! 
{
    "bclconvert_report_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "instrument_run_id": "string",
    "interop_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Outputs Template

Click to expand! 
{
    "interop_output_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "multiqc_html_report": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "multiqc_output_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand! 
[
    "workflow.cwl#bclconvert-interop-qc--1.3.1--1.21/generate_interop_qc_step",
    "workflow.cwl#bclconvert-interop-qc--1.3.1--1.21/run_multiqc_step"
]

Packed workflow

Click to expand! 
[
    "#main/generate_interop_qc_step",
    "#main/run_multiqc_step"
]

Inputs

Click to expand!

BCLConvert Report Directory

ID: bclconvert_report_directory

Optional: False
Type: Directory
Docs:
The output directory from a BCLConvert run named 'Reports'

Instrument Run ID

ID: instrument_run_id

Optional: False
Type: string
Docs:
The instrument run ID

Interop Directory

ID: interop_directory

Optional: False
Type: Directory
Docs:
The interop directory

Steps

Click to expand!

Generate InterOp QC

ID: bclconvert-interop-qc--1.3.1--1.21/generate_interop_qc_step

Step Type: tool
Docs:

Generate the interop files by mounting the interop directory underneath a directory named by the run id specified.
along with the run info xml file.

Get RunInfo.xml file from Reports Dir

ID: bclconvert-interop-qc--1.3.1--1.21/get_run_info_xml_file_from_reports_dir

Step Type: expression
Docs:

Get the RunInfo.xml file from the Reports Directory

Run Multiqc

ID: bclconvert-interop-qc--1.3.1--1.21/run_multiqc_step

Step Type: tool
Docs:

Run MultiQC on the input reports directory along with the generated index summary files

Outputs

Click to expand!

interop out dir

ID: bclconvert-interop-qc--1.3.1--1.21/interop_output_dir

Optional: False
Output Type: Directory
Docs:
Directory containing the inteop summary csvs

multiqc html report

ID: bclconvert-interop-qc--1.3.1--1.21/multiqc_html_report

Optional: False
Output Type: File
Docs:
The HTML report generated by the multiqc step

multiqc output dir

ID: bclconvert-interop-qc--1.3.1--1.21/multiqc_output_dir

Optional: False
Output Type: Directory
Docs:
Directory containing the multiqc data

Assets 10
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