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Added the samtools/dict module (#1922)
* Added the samtools/dict module * samtools/dict is single-threaded
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44
modules/samtools/dict/main.nf
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44
modules/samtools/dict/main.nf
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process SAMTOOLS_DICT {
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tag "$fasta"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.15.1--h1170115_0' :
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'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
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input:
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tuple val(meta), path(fasta)
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output:
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tuple val(meta), path ("*.dict"), emit: dict
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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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script:
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def args = task.ext.args ?: ''
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"""
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samtools \\
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dict \\
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$args \\
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$fasta \\
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> ${fasta}.dict
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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stub:
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"""
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touch ${fasta}.dict
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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41
modules/samtools/dict/meta.yml
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41
modules/samtools/dict/meta.yml
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name: samtools_dict
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description: Create a sequence dictionary file from a FASTA file
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keywords:
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- dict
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- fasta
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: http://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- fasta:
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type: file
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description: FASTA file
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pattern: "*.{fa,fasta}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- dict:
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type: file
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description: FASTA dictionary file
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pattern: "*.{dict}"
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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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- "@muffato"
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@ -1919,6 +1919,10 @@ samtools/depth:
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- modules/samtools/depth/**
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- tests/modules/samtools/depth/**
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samtools/dict:
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- modules/samtools/dict/**
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- tests/modules/samtools/dict/**
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samtools/faidx:
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- modules/samtools/faidx/**
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- tests/modules/samtools/faidx/**
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13
tests/modules/samtools/dict/main.nf
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13
tests/modules/samtools/dict/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_DICT } from '../../../../modules/samtools/dict/main.nf'
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workflow test_samtools_dict {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
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SAMTOOLS_DICT ( input )
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}
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5
tests/modules/samtools/dict/nextflow.config
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5
tests/modules/samtools/dict/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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}
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13
tests/modules/samtools/dict/test.yml
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13
tests/modules/samtools/dict/test.yml
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- name: samtools dict test_samtools_dict
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command: nextflow run tests/modules/samtools/dict -entry test_samtools_dict -c tests/config/nextflow.config -c tests/modules/samtools/dict/nextflow.config
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tags:
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- samtools
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- samtools/dict
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files:
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- path: output/samtools/genome.fasta.dict
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contains:
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- "SN:MT192765.1"
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- "LN:29829"
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- "M5:c95f3e5592d0ad9974e41e7f0ea14eb0"
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- path: output/samtools/versions.yml
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md5sum: 12cd0c5ce466eefb2dff72625ecbe5c2
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