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Update minimap2/align module (#1537)
This commit is contained in:
Sofia Stamouli
GitHub
parent
6a46e7cf11
commit
1f77bc130b
4 changed files with 50 additions and 16 deletions
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@ -2,18 +2,22 @@ process MINIMAP2_ALIGN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? 'bioconda::minimap2=2.21' : null)
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conda (params.enable_conda ? 'bioconda::minimap2=2.21 bioconda::samtools=1.12' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/minimap2:2.21--h5bf99c6_0' :
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'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
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'https://depot.galaxyproject.org/singularity/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' :
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'quay.io/biocontainers/mulled-v2-66534bcbb7031a148b13e2ad42583020b9cd25c4:1679e915ddb9d6b4abda91880c4b48857d471bd8-0' }"
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input:
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tuple val(meta), path(reads)
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path reference
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val bam_format
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val cigar_paf_format
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val cigar_bam
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output:
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tuple val(meta), path("*.paf"), emit: paf
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.paf"), optional: true, emit: paf
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tuple val(meta), path("*.bam"), optional: true, emit: bam
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -22,13 +26,19 @@ process MINIMAP2_ALIGN {
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
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def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
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def cigar_paf = cigar_paf_format && !sam_format ? "-c" : ''
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def set_cigar_bam = cigar_bam && sam_format ? "-L" : ''
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"""
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minimap2 \\
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$args \\
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-t $task.cpus \\
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$reference \\
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$input_reads \\
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> ${prefix}.paf
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$cigar_paf \\
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$set_cigar_bam \\
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$bam_output
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -29,6 +29,17 @@ input:
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type: file
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description: |
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Reference database in FASTA format.
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- bam_format:
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type: boolean
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description: Specify that output should be in BAM format
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- cigar_paf_format:
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type: boolean
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description: Specify that output CIGAR should be in PAF format
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- cigar_bam:
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type: boolean
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description: |
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Write CIGAR with >65535 ops at the CG tag. This is recommended when
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doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
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output:
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- meta:
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type: map
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@ -39,9 +50,16 @@ output:
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type: file
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description: Alignment in PAF format
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pattern: "*.paf"
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- bam:
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type: file
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description: Alignment in BAM format
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pattern: "*.bam"
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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authors:
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- "@heuermh"
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- "@sofstam"
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- "@sateeshperi"
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- "@jfy133"
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@ -9,8 +9,11 @@ workflow test_minimap2_align_single_end {
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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bam_format = true
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cigar_paf_format = false
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cigar_bam = false
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MINIMAP2_ALIGN ( input, fasta )
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MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam)
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}
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workflow test_minimap2_align_paired_end {
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@ -19,6 +22,9 @@ workflow test_minimap2_align_paired_end {
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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bam_format = true
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cigar_paf_format = false
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cigar_bam = false
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MINIMAP2_ALIGN ( input, fasta )
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MINIMAP2_ALIGN ( input, fasta, bam_format, cigar_paf_format, cigar_bam )
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}
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@ -1,17 +1,17 @@
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- name: minimap2 align single-end
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command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
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- name: minimap2 align test_minimap2_align_single_end
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command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_single_end -c tests/config/nextflow.config
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tags:
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- minimap2
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- minimap2/align
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files:
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- path: ./output/minimap2/test.paf
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md5sum: 70e8cf299ee3ecd33e629d10c1f588ce
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- path: output/minimap2/test.bam
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- path: output/minimap2/versions.yml
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- name: minimap2 align paired-end
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command: nextflow run ./tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/minimap2/align/nextflow.config
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- name: minimap2 align test_minimap2_align_paired_end
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command: nextflow run tests/modules/minimap2/align -entry test_minimap2_align_paired_end -c tests/config/nextflow.config
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tags:
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- minimap2
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- minimap2/align
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files:
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- path: ./output/minimap2/test.paf
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md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28
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- path: output/minimap2/test.bam
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- path: output/minimap2/versions.yml
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