mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
Merge branch 'master' into new-module-rtg/vcfeval
This commit is contained in:
commit
aceb5220cf
13 changed files with 200 additions and 48 deletions
34
modules/meryl/histogram/main.nf
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34
modules/meryl/histogram/main.nf
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@ -0,0 +1,34 @@
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process MERYL_HISTOGRAM {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
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'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
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input:
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tuple val(meta), path(meryl_db)
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output:
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tuple val(meta), path("*.hist"), emit: hist
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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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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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meryl histogram \\
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threads=$task.cpus \\
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$args \\
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$meryl_db > ${prefix}.hist
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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meryl: \$( meryl --version |& sed 's/meryl //' )
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END_VERSIONS
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"""
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}
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41
modules/meryl/histogram/meta.yml
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41
modules/meryl/histogram/meta.yml
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@ -0,0 +1,41 @@
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name: "meryl_histogram"
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description: A genomic k-mer counter (and sequence utility) with nice features.
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keywords:
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- k-mer
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- histogram
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tools:
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- "meryl":
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description: "A genomic k-mer counter (and sequence utility) with nice features. "
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homepage: "https://github.com/marbl/meryl"
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documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
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tool_dev_url: "https://github.com/marbl/meryl"
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doi: ""
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licence: "['GPL']"
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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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- meryl_dbs:
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type: directory
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description: Meryl k-mer database
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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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- 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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- hist:
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type: file
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description: Histogram of k-mers
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pattern: "*.hist"
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authors:
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- "@mahesh-panchal"
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@ -1,5 +1,4 @@
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//There is a -L option to only output alignments in interval, might be an option for exons/panel data?
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process SAMTOOLS_BAMTOCRAM {
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process SAMTOOLS_CONVERT {
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tag "$meta.id"
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label 'process_medium'
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@ -14,8 +13,8 @@ process SAMTOOLS_BAMTOCRAM {
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path fai
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output:
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tuple val(meta), path("*.cram"), path("*.crai"), emit: cram_crai
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path "versions.yml" , emit: versions
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tuple val(meta), path("*.{cram,bam}"), path("*.{crai,bai}") , emit: alignment_index
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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@ -23,9 +22,17 @@ process SAMTOOLS_BAMTOCRAM {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def output_extension = input.getExtension() == "bam" ? "cram" : "bam"
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"""
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samtools view --threads ${task.cpus} --reference ${fasta} -C $args $input > ${prefix}.cram
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samtools index -@${task.cpus} ${prefix}.cram
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samtools view \\
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--threads ${task.cpus} \\
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--reference ${fasta} \\
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$args \\
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$input \\
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-o ${prefix}.${output_extension}
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samtools index -@${task.cpus} ${prefix}.${output_extension}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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@ -1,5 +1,5 @@
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name: samtools_bamtocram
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description: filter/convert and then index CRAM file
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name: samtools_convert
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description: convert and then index CRAM -> BAM or BAM -> CRAM file
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keywords:
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- view
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- index
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@ -23,12 +23,12 @@ input:
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e.g. [ id:'test', single_end:false ]
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- input:
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type: file
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description: BAM/SAM file
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pattern: "*.{bam,sam}"
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- index:
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type: file
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description: BAM/SAM index file
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pattern: "*.{bai,sai}"
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description: BAM/CRAM index file
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pattern: "*.{bai,crai}"
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- fasta:
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type: file
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description: Reference file to create the CRAM file
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@ -39,10 +39,10 @@ output:
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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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- cram_crai:
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- alignment_index:
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type: file
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description: filtered/converted CRAM file + index
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pattern: "*{.cram,.crai}"
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description: filtered/converted BAM/CRAM file + index
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pattern: "*{.bam/cram,.bai/crai}"
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- version:
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type: file
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description: File containing software version
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@ -1218,6 +1218,10 @@ meryl/count:
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- modules/meryl/count/**
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- tests/modules/meryl/count/**
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meryl/histogram:
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- modules/meryl/histogram/**
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- tests/modules/meryl/histogram/**
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metabat2/jgisummarizebamcontigdepths:
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- modules/metabat2/jgisummarizebamcontigdepths/**
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- tests/modules/metabat2/jgisummarizebamcontigdepths/**
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@ -1635,9 +1639,9 @@ samtools/bam2fq:
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- modules/samtools/bam2fq/**
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- tests/modules/samtools/bam2fq/**
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samtools/bamtocram:
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- modules/samtools/bamtocram/**
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- tests/modules/samtools/bamtocram/**
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samtools/convert:
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- modules/samtools/convert/**
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- tests/modules/samtools/convert/**
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samtools/collatefastq:
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- modules/samtools/collatefastq/**
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@ -1771,14 +1775,14 @@ slimfastq:
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- modules/slimfastq/**
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- tests/modules/slimfastq/**
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snapaligner/index:
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- modules/snapaligner/index/**
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- tests/modules/snapaligner/index/**
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snapaligner/align:
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- modules/snapaligner/align/**
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- tests/modules/snapaligner/align/**
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snapaligner/index:
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- modules/snapaligner/index/**
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- tests/modules/snapaligner/index/**
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snpdists:
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- modules/snpdists/**
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- tests/modules/snpdists/**
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17
tests/modules/meryl/histogram/main.nf
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17
tests/modules/meryl/histogram/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MERYL_COUNT } from '../../../../modules/meryl/count/main.nf'
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include { MERYL_HISTOGRAM } from '../../../../modules/meryl/histogram/main.nf'
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workflow test_meryl_histogram {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
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]
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MERYL_COUNT ( input )
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MERYL_HISTOGRAM ( MERYL_COUNT.out.meryl_db )
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}
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@ -1,5 +1,6 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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ext.args = 'k=21'
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}
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10
tests/modules/meryl/histogram/test.yml
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10
tests/modules/meryl/histogram/test.yml
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- name: meryl histogram test_meryl_histogram
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command: nextflow run tests/modules/meryl/histogram -entry test_meryl_histogram -c tests/config/nextflow.config
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tags:
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- meryl/histogram
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- meryl
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files:
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- path: output/meryl/test.hist
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md5sum: 4bfdc8b287ee0cfd9922bbfa8cd64650
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- path: output/meryl/versions.yml
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md5sum: 050038f1b1df79977a393cce1b4b2ddb
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@ -1,17 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/bamtocram/main.nf'
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workflow test_samtools_bamtocram {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
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}
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@ -1,9 +0,0 @@
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- name: samtools bamtocram test_samtools_bamtocram
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command: nextflow run ./tests/modules/samtools/bamtocram -entry test_samtools_bamtocram -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bamtocram/nextflow.config
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tags:
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- samtools/bamtocram
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- samtools
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files:
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- path: output/samtools/test.cram
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- path: output/samtools/test.cram.crai
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- path: output/samtools/versions.yml
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31
tests/modules/samtools/convert/main.nf
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31
tests/modules/samtools/convert/main.nf
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@ -0,0 +1,31 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_CONVERT as SAMTOOLS_BAMTOCRAM } from '../../../../modules/samtools/convert/main.nf'
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include { SAMTOOLS_CONVERT as SAMTOOLS_CRAMTOBAM } from '../../../../modules/samtools/convert/main.nf'
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workflow test_samtools_convert_bamtocram {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_BAMTOCRAM ( input, fasta, fai )
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}
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workflow test_samtools_convert_cramtobam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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SAMTOOLS_CRAMTOBAM ( input, fasta, fai )
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}
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12
tests/modules/samtools/convert/nextflow.config
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12
tests/modules/samtools/convert/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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withName:SAMTOOLS_BAMTOCRAM{
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ext.args = "-C"
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}
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withName:SAMTOOLS_CRAMTOBAM{
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ext.args = "-b"
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}
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}
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21
tests/modules/samtools/convert/test.yml
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21
tests/modules/samtools/convert/test.yml
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@ -0,0 +1,21 @@
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- name: samtools convert test_samtools_convert_bamtocram
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command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_bamtocram -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools/convert
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files:
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- path: output/samtools/test.cram
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- path: output/samtools/test.cram.crai
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- path: output/samtools/versions.yml
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- name: samtools convert test_samtools_convert_cramtobam
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command: nextflow run tests/modules/samtools/convert -entry test_samtools_convert_cramtobam -c tests/config/nextflow.config
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tags:
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- samtools
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- samtools/convert
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files:
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- path: output/samtools/test.bam
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md5sum: c262b6dc15f9b480bdb47d6d018b4b56
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- path: output/samtools/test.bam.bai
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md5sum: 6e8f5034f728401bfa841c8e70c62463
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- path: output/samtools/versions.yml
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