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@github-actions github-actions released this 08 Jul 03:51
· 238 commits to main since this release
dragen-alignment-pipeline/4.2.4__20240708034912
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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__20240708034912 / Bundle Version v9_r3__20240708034912

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__20240708034912.

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

Bundle ID: 9f1ead06-ba94-4857-b50f-5fcb9e716609

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 71f094dc-0cf8-4fcf-890c-9f3edf00ee20
    Pipeline Code: dragen-alignment-pipeline__4_2_4__20240708034912

Projects

  • development
  • staging

Datasets

  • dragen_hash_table_v9_r3_alt_masked_cnv_hla_rna
  • hg38_v39_gencode_annotation
  • wgs_validation_fastq__cups_pair_8
  • wgs_validation_fastq__2016_249_17_MH_P033
  • wgs_validation_fastq__2016_249_18_WH_P025
  • wgs_validation_fastq__B_ALL_Case_10
  • wgs_validation_fastq_Diploid_Never_Responder
  • wgs_validation_fastq_SBJ00303
  • wgs_validation_fastq_SEQC50
  • wgs_validation_fastq_SFRC01073
  • wts_validation_fastq__SBJ00480
  • wts_validation_fastq__SBJ00028
  • wts_validation_fastq__SBJ00061
  • wts_validation_fastq__SBJ00188
  • wts_validation_fastq__SBJ00199
  • wts_validation_fastq__SBJ00236
  • wts_validation_fastq__SBJ00238

Bundle Name: dragen_alignment_pipeline_prod__4_2_4__20240708034912 / Bundle Version v9_r3__20240708034912

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__20240708034912.

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

Bundle ID: 218726be-7f1a-4847-96ae-48a1f2caf882

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 71f094dc-0cf8-4fcf-890c-9f3edf00ee20
    Pipeline Code: dragen-alignment-pipeline__4_2_4__20240708034912

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__20240708034912/dragen-alignment-pipeline__4.2.4__20240708034912.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_coeff: string

# mismatch pen (Optional)
# Docs: Score penalty for a mismatch.
mismatch_pen: string

# no unclip score (Optional)
# Docs: When no-unclip-score is set to 1, any unclipped bonus (unclip-score) contributing to an alignment is removed from the alignment score before further processing.
no_unclip_score: false

# no unpaired (Optional)
# Docs: If only properly paired alignments should be reported for paired reads.
no_unpaired: false

# output directory (Required)
# Docs: The directory where all output files are placed
output_directory: string

# output file prefix (Required)
# Docs: The prefix given to all output files
output_file_prefix: string

# pe max penalty (Optional)
# Docs: Maximum pairing score penalty, for unpaired or distant ends.
# Range: 0-255
pe_max_penalty: string

# pe orientation (Optional)
# Docs: Expected paired-end orientation: 0=FR, 1=RF, 2=FF.
pe_orientation: '0'

# preserve map align order (Optional)
# Docs: Produce output file that preserves original order of reads in the input file.
preserve_map_align_order: false

# reference tar (Required)
# Docs: Path to ref data tarball
reference_tar:
  class: File
  location: icav2://project_id/path/to/file

# remove duplicates (Optional)
# Docs: If true, remove duplicate alignment records instead of just flagging them.
remove_duplicates: false

# rescue sigmas (Optional)
# Docs: Deviations from the mean read length used for rescue scan radius. Default is 2.5.
rescue_sigmas: string

# sec aligns (Optional)
# Docs: Maximum secondary (suboptimal) alignments to report per read.
# Range: 0 - 30
sec_aligns: string

# sec aligns hard (Optional)
# Docs: Set to force unmapped when not all secondary alignments can be output.
sec_aligns_hard: false

# sec phred delta (Optional)
# Docs: Only secondary alignments with likelihood within this Phred of the primary are reported.
# Range: 0 - 255
sec_phred_delta: string

# sec score delta (Optional)
# Docs: Secondary aligns allowed with pair score no more than this far below primary.
sec_score_delta: string

# seed density (Optional)
# Docs: Requested density of seeds from reads queried in the hash table
# Range: 0 - 1
seed_density: string

# supp aligns (Optional)
# Docs: Maximum supplementary (chimeric) alignments to report per read.
supp_aligns: string

# supp as sec (Optional)
# Docs: If supplementary alignments should be reported with secondary flag.
supp_as_sec: false

# supp min score adj (Optional)
# Docs: Amount to increase minimum alignment score for supplementary alignments.
# This score is computed by host software as "8 * match-score" for DNA, and is default 0 for RNA.
supp_min_score_adj: string

# unclip score (Optional)
# Docs: Score bonus for reaching each edge of the read.
# Range: 0 - 127
unclip_score: string

# unpaired pen (Optional)
# Docs: Penalty for unpaired alignments in Phred scale.
# Range: 0 - 255
unpaired_pen: string

# verbose (Optional)
# Docs: Enable verbose output from DRAGEN.
verbose: false

Json

Click to expand! 
{
    "aln_min_score": "string",
    "alt_aware": false,
    "ann_sj_max_indel": "string",
    "annotation_file": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "dedup_min_qual": "string",
    "edit_chain_limit": "string",
    "edit_mode": "0",
    "edit_read_len": "string",
    "edit_seed_num": "string",
    "en_alt_hap_aln": false,
    "en_chimeric_aln": false,
    "enable_duplicate_marking": false,
    "enable_map_align": false,
    "enable_map_align_output": false,
    "enable_rna": false,
    "enable_rna_quantification": false,
    "enable_rrna_filter": false,
    "enable_sort": false,
    "fastq_list": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "fastq_list_rows": [
        {
            "rgid": "string",
            "rglb": "string",
            "rgsm": "string",
            "lane": "string",
            "read_1": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            },
            "read_2": {
                "class": "File",
                "location": "icav2://project_id/path/to/file"
            }
        }
    ],
    "gap_ext_pen": "string",
    "gap_open_pen": "string",
    "generate_md_tags": false,
    "generate_sa_tags": false,
    "generate_zs_tags": false,
    "global": false,
    "hard_clips": "string",
    "map_orientations": "0",
    "mapq_max": "string",
    "mapq_strict_js": false,
    "match_n_score": "string",
    "match_score": "string",
    "max_intron_bases": "string",
    "max_rescues": "string",
    "min_intron_bases": "string",
    "min_score_coeff": "string",
    "mismatch_pen": "string",
    "no_unclip_score": false,
    "no_unpaired": false,
    "output_directory": "string",
    "output_file_prefix": "string",
    "pe_max_penalty": "string",
    "pe_orientation": "0",
    "preserve_map_align_order": false,
    "reference_tar": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "remove_duplicates": false,
    "rescue_sigmas": "string",
    "sec_aligns": "string",
    "sec_aligns_hard": false,
    "sec_phred_delta": "string",
    "sec_score_delta": "string",
    "seed_density": "string",
    "supp_aligns": "string",
    "supp_as_sec": false,
    "supp_min_score_adj": "string",
    "unclip_score": "string",
    "unpaired_pen": "string",
    "verbose": false
}

Outputs Template

Click to expand! 
{
    "dragen_alignment_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "dragen_bam_out": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "multiqc_output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand! 
[
    "workflow.cwl#dragen-alignment-pipeline--4.2.4/create_dummy_file_step",
    "workflow.cwl#dragen-alignment-pipeline--4.2.4/dragen_qc_step",
    "workflow.cwl#dragen-alignment-pipeline--4.2.4/run_dragen_alignment_step"
]

Packed workflow

Click to expand! 
[
    "#main/create_dummy_file_step",
    "#main/dragen_qc_step",
    "#main/run_dragen_alignment_step"
]

Inputs

Click to expand!

aln min score

ID: aln_min_score

Optional: True
Type: int
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

alt aware

ID: alt_aware

Optional: True
Type: boolean
Docs:
Enables special processing for alt contigs, if alt liftover was used in hash table.
Enabled by default if reference was built with liftover.

ann sj max indel

ID: ann_sj_max_indel

Optional: True
Type: int
Docs:
Maximum indel length to expect near an annotated splice junction.
Range: 0 - 63

annotation file

ID: annotation_file

Optional: True
Type: File
Docs:
Use to supply a gene annotation file. Required for quantification and gene-fusion.

dedup min qual

ID: dedup_min_qual

Optional: True
Type: int
Docs:
Minimum base quality for calculating read quality metric for deduplication.
Range: 0-63

edit chain limit

ID: edit_chain_limit

Optional: True
Type: int
Docs:
For edit-mode 1 or 2: Maximum seed chain length in a read to qualify for seed editing.
Range: > 0

edit mode

ID: edit_mode

Optional: True
Type: [ 0 | 1 | 2 | 3 ]
Docs:
0 = No edits, 1 = Chain len test, 2 = Paired chain len test, 3 = Edit all std seeds.

edit read len

ID: edit_read_len

Optional: True
Type: int
Docs:
For edit-mode 1 or 2: Read length in which to try edit-seed-num edited seeds.
Range: > 0

edit seed num

ID: edit_seed_num

Optional: True
Type: int
Docs:
For edit-mode 1 or 2: Requested number of seeds per read to allow editing on.
Range: > 0

en alt hap aln

ID: en_alt_hap_aln

Optional: True
Type: boolean
Docs:
Allows chimeric alignments to be output, as supplementary.

en chimeric aln

ID: en_chimeric_aln

Optional: True
Type: boolean
Docs:
Allows chimeric alignments to be output, as supplementary.

enable duplicate marking

ID: enable_duplicate_marking

Optional: True
Type: boolean
Docs:
Enable the flagging of duplicate output alignment records.

enable map align

ID: enable_map_align

Optional: True
Type: boolean
Docs:
Enable use of BAM input files for mapper/aligner.

enable map align

ID: enable_map_align_output

Optional: True
Type: boolean
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 rna

ID: enable_rna

Optional: True
Type: boolean
Docs:
Enable rna specific settings

enable rna quantification

ID: enable_rna_quantification

Optional: True
Type: boolean
Docs:
If set to true, enables RNA quantification. Requires --enable-rna to be set to true.

enable rrna filtering

ID: enable_rrna_filter

Optional: True
Type: boolean
Docs:
Use the DRAGEN RNA pipeline to filter rRNA reads during alignment. The default value is false.

enable sort

ID: enable_sort

Optional: True
Type: boolean
Docs:
Enable sorting after mapping/alignment.

fastq list

ID: fastq_list

Optional: True
Type: File
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)

Row of fastq lists

ID: fastq_list_rows

Optional: True
Type: fastq-list-row[]
Docs:
The row of fastq lists.
Each row has the following attributes:

  • RGID
  • RGLB
  • RGSM
  • Lane
  • Read1File
  • Read2File (optional)

gap ext pen

ID: gap_ext_pen

Optional: True
Type: int
Docs:
Score penalty for gap extension.

gap open pen

ID: gap_open_pen

Optional: True
Type: int
Docs:
Score penalty for opening a gap (insertion or deletion).

generate md tags

ID: generate_md_tags

Optional: True
Type: boolean
Docs:
Whether to generate MD tags with alignment output records. Default is false.

generate sa tags

ID: generate_sa_tags

Optional: True
Type: boolean
Docs:
Whether to generate SA:Z tags for records that have chimeric/supplemental alignments.

generate zs tags

ID: generate_zs_tags

Optional: True
Type: boolean
Docs:
Whether to generate ZS tags for alignment output records. Default is false.

global

ID: global

Optional: True
Type: boolean
Docs:
If alignment is global (Needleman-Wunsch) rather than local (Smith-Waterman).

hard clips

ID: hard_clips

Optional: True
Type: int
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.

map orientations

ID: map_orientations

Optional: True
Type: [ 0 | 1 | 2 ]
Docs:
Constrain orientations to accept forward-only, reverse-complement only, or any alignments.

mapq max

ID: mapq_max

Optional: True
Type: int
Docs:
Ceiling on reported MAPQ. Max 255

mapq strict js

ID: mapq_strict_js

Optional: True
Type: boolean
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.

match n score

ID: match_n_score

Optional: True
Type: int
Docs:
(signed) Score increment for matching a reference 'N' nucleotide IUB code.
Range: -16 to 15

match score

ID: match_score

Optional: True
Type: float
Docs:
Score increment for matching reference nucleotide.
When global = 0, match-score > 0; When global = 1, match-score >= 0

max intron bases

ID: max_intron_bases

Optional: True
Type: int
Docs:
Maximum intron length reported.

max rescues

ID: max_rescues

Optional: True
Type: int
Docs:
Maximum rescue alignments per read pair. Default is 10

min intron bases

ID: min_intron_bases

Optional: True
Type: int
Docs:
Minimum reference deletion length reported as an intron.

min score coeff

ID: min_score_coeff

Optional: True
Type: float
Docs:
Adjustment to aln-min-score per read base.
Range: -64 to 63.999

mismatch pen

ID: mismatch_pen

Optional: True
Type: int
Docs:
Score penalty for a mismatch.

no unclip score

ID: no_unclip_score

Optional: True
Type: boolean
Docs:
When no-unclip-score is set to 1, any unclipped bonus (unclip-score) contributing to an alignment is removed from the alignment score before further processing.

no unpaired

ID: no_unpaired

Optional: True
Type: boolean
Docs:
If only properly paired alignments should be reported for paired reads.

output directory

ID: output_directory

Optional: False
Type: string
Docs:
The directory where all output files are placed

output file prefix

ID: output_file_prefix

Optional: False
Type: string
Docs:
The prefix given to all output files

pe max penalty

ID: pe_max_penalty

Optional: True
Type: int
Docs:
Maximum pairing score penalty, for unpaired or distant ends.
Range: 0-255

pe orientation

ID: pe_orientation

Optional: True
Type: [ 0 | 1 | 2 ]
Docs:
Expected paired-end orientation: 0=FR, 1=RF, 2=FF.

preserve map align order

ID: preserve_map_align_order

Optional: True
Type: boolean
Docs:
Produce output file that preserves original order of reads in the input file.

reference tar

ID: reference_tar

Optional: False
Type: File
Docs:
Path to ref data tarball

remove duplicates

ID: remove_duplicates

Optional: True
Type: boolean
Docs:
If true, remove duplicate alignment records instead of just flagging them.

rescue sigmas

ID: rescue_sigmas

Optional: True
Type: float
Docs:
Deviations from the mean read length used for rescue scan radius. Default is 2.5.

sec aligns

ID: sec_aligns

Optional: True
Type: int
Docs:
Maximum secondary (suboptimal) alignments to report per read.
Range: 0 - 30

sec aligns hard

ID: sec_aligns_hard

Optional: True
Type: boolean
Docs:
Set to force unmapped when not all secondary alignments can be output.

sec phred delta

ID: sec_phred_delta

Optional: True
Type: int
Docs:
Only secondary alignments with likelihood within this Phred of the primary are reported.
Range: 0 - 255

sec score delta

ID: sec_score_delta

Optional: True
Type: float
Docs:
Secondary aligns allowed with pair score no more than this far below primary.

seed density

ID: seed_density

Optional: True
Type: float
Docs:
Requested density of seeds from reads queried in the hash table
Range: 0 - 1

supp aligns

ID: supp_aligns

Optional: True
Type: int
Docs:
Maximum supplementary (chimeric) alignments to report per read.

supp as sec

ID: supp_as_sec

Optional: True
Type: boolean
Docs:
If supplementary alignments should be reported with secondary flag.

supp min score adj

ID: supp_min_score_adj

Optional: True
Type: float
Docs:
Amount to increase minimum alignment score for supplementary alignments.
This score is computed by host software as "8 * match-score" for DNA, and is default 0 for RNA.

unclip score

ID: unclip_score

Optional: True
Type: int
Docs:
Score bonus for reaching each edge of the read.
Range: 0 - 127

unpaired pen

ID: unpaired_pen

Optional: True
Type: int
Docs:
Penalty for unpaired alignments in Phred scale.
Range: 0 - 255

verbose

ID: verbose

Optional: True
Type: boolean
Docs:
Enable verbose output from DRAGEN.

Steps

Click to expand!

Create dummy file

ID: dragen-alignment-pipeline--4.2.4/create_dummy_file_step

Step Type: tool
Docs:

Intermediate step for letting multiqc-interop be placed in stream mode

dragen qc step

ID: dragen-alignment-pipeline--4.2.4/dragen_qc_step

Step Type: tool
Docs:

The dragen qc step - this takes in an array of dirs

run dragen alignment step

ID: dragen-alignment-pipeline--4.2.4/run_dragen_alignment_step

Step Type: tool
Docs:

Runs the alignment step on a dragen fpga
Takes in a fastq list and corresponding mount paths from the predefined mount paths
All other options available at the top of the workflow

Outputs

Click to expand!

dragen alignment output directory

ID: dragen-alignment-pipeline--4.2.4/dragen_alignment_output_directory

Optional: False
Output Type: Directory
Docs:
The output directory containing all alignment output files and qc metrics

dragen bam out

ID: dragen-alignment-pipeline--4.2.4/dragen_bam_out

Optional: False
Output Type: File
Docs:
The output alignment file

dragen QC report out

ID: dragen-alignment-pipeline--4.2.4/multiqc_output_directory

Optional: False
Output Type: Directory
Docs:
The dragen multiQC output

Assets 10
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