mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 21:43:09 +00:00
Remove flagstat as bowtie2 reports this itself
This commit is contained in:
parent
482112bb42
commit
066ceb2bca
9 changed files with 72 additions and 116 deletions
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@ -132,7 +132,6 @@ process {
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]
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}
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withName: PORECHOP {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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@ -142,6 +141,24 @@ process {
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]
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}
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withName: BOWTIE2_BUILD {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/build" },
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mode: 'copy',
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pattern: '*.bt2'
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]
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}
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withName: BOWTIE2_ALIGN {
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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path: { "${params.outdir}/bowtie2/align" },
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mode: 'copy',
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pattern: '*.{fastq.gz,bam}'
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]
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}
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withName: CAT_FASTQ {
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publishDir = [
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path: { "${params.outdir}/prepared_sequences" },
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@ -27,5 +27,7 @@ params {
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run_kraken2 = true
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run_malt = true
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shortread_clipmerge = true
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shortread_hostremoval = true
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shortread_hostremoval_reference = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
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}
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@ -36,9 +36,6 @@
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"porechop": {
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"git_sha": "e20e57f90b6787ac9a010a980cf6ea98bd990046"
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},
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"samtools/flagstat": {
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"git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
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},
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"untar": {
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"git_sha": "e080f4c8acf5760039ed12ec1f206170f3f9a918"
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}
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34
modules/nf-core/modules/samtools/flagstat/main.nf
generated
34
modules/nf-core/modules/samtools/flagstat/main.nf
generated
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@ -1,34 +0,0 @@
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process SAMTOOLS_FLAGSTAT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::samtools=1.15" : 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--h1170115_1' :
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'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
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input:
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tuple val(meta), path(bam), path(bai)
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output:
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tuple val(meta), path("*.flagstat"), emit: flagstat
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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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flagstat \\
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--threads ${task.cpus-1} \\
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$bam \\
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> ${bam}.flagstat
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cat <<-END_VERSIONS > versions.yml
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"${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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49
modules/nf-core/modules/samtools/flagstat/meta.yml
generated
49
modules/nf-core/modules/samtools/flagstat/meta.yml
generated
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@ -1,49 +0,0 @@
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name: samtools_flagstat
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description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
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keywords:
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- stats
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- mapping
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- counts
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- bam
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- sam
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- cram
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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: hhttp://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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- bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- bai:
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type: file
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description: Index for BAM/CRAM/SAM file
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pattern: "*.{bai,crai,sai}"
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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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- flagstat:
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type: file
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description: File containing samtools flagstat output
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pattern: "*.{flagstat}"
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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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- "@drpatelh"
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@ -66,6 +66,7 @@ params {
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longread_clip = false
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// Host Removal
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shortread_hostremoval = false
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shortread_hostremoval_reference = null
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shortread_hostremoval_index = null
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@ -266,8 +266,7 @@
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"type": "boolean"
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},
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"shortread_clipmerge_excludeunmerged": {
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"type": "boolean",
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"default": false
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"type": "boolean"
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},
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"longread_clip": {
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"type": "boolean"
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@ -304,6 +303,17 @@
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"shortread_clipmerge_minlength": {
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"type": "integer",
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"default": 15
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},
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"shortread_hostremoval": {
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"type": "boolean"
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},
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"shortread_hostremoval_reference": {
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"type": "string",
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"default": null
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},
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"shortread_hostremoval_index": {
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"type": "string",
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"default": null
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}
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}
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}
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@ -2,34 +2,29 @@
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// Remove host reads via alignment and export off-target reads
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//
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include { BOWTIE2_ALIGN } from '../../../modules/nf-core/modules/bowtie2/align/main'
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include { BOWTIE2_BUILD } from '../../../modules/nf-core/modules/bowtie2/build/main'
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include { SAMTOOLS_VIEW } from '../../../modules/nf-core/modules/samtools/view/main'
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include { SAMTOOLS_FASTQ } from '../../../modules/nf-core/modules/samtools/fastq/main'
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include { SAMTOOLS_FLAGSTAT } from '../../../modules/nf-core/modules/samtools/flagstat/main'
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include { BOWTIE2_BUILD } from '../../modules/nf-core/modules/bowtie2/build/main'
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include { BOWTIE2_ALIGN } from '../../modules/nf-core/modules/bowtie2/align/main'
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workflow SHORTREAD_PREPROCESSING {
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workflow SHORTREAD_HOSTREMOVAL {
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take:
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reads // [ [ meta ], [ reads ] ]
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reference // /path/to/fasta
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index // /path/to/index
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main:
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ch_versions = Channel.empty()
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ch_multiqc_files = Channel.empty()
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if ( !params.shortread_hostremoval_index ) {
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file( , checkIfExists: true )
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BOWTIE2_BUILD ( reference )
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ch_bowtie2_index = BOWTIE2_BUILD ( reference ).index
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ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
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} else {
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ch_bowtie2_index = index.first()
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}
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BOWTIE2_ALIGN ( reads, BOWTIE2_BUILD.out.index )
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ch_versions = ch_versions.mix( BOWTIE2_BUILD.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.log )
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SAMTOOLS_FLAGSTAT ( BOWTIE2_ALIGN.out.bam )
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ch_versions = ch_versions.mix( SAMTOOLS_FLAGSTAT.out.versions )
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ch_multiqc_files = ch_multiqc_files.mix( SAMTOOLS_FLAGSTAT.out.flagstat )
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BOWTIE2_ALIGN ( reads, ch_bowtie2_index, true )
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ch_versions = ch_versions.mix( BOWTIE2_ALIGN.out.versions.first() )
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ch_multiqc_files = ch_multiqc_files.mix( BOWTIE2_ALIGN.out.log )
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emit:
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reads = BOWTIE2_ALIGN.out.fastq // channel: [ val(meta), [ reads ] ]
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@ -23,8 +23,11 @@ if (params.shortread_clipmerge_mergepairs && params.run_malt ) log.warn "[nf-cor
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if (params.shortread_clipmerge_excludeunmerged && !params.shortread_clipmerge_mergepairs) exit 1, "[nf-core/taxprofiler] error: cannot include unmerged reads when merging not turned on. Please specify --shortread_clipmerge_mergepairs"
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// TODO Add check if index but no reference exit 1
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { }
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if (params.shortread_hostremoval_index) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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if (params.shortread_hostremoval && !params.shortread_hostremoval_reference) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval requested but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (!params.shortread_hostremoval_reference && params.shortread_hostremoval_reference_index) { exit 1, "[nf-core/taxprofiler] error: --shortread_hostremoval_index provided but no --shortread_hostremoval_reference FASTA supplied. Check input." }
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if (params.shortread_hostremoval_reference ) { ch_reference = file(params.shortread_hostremoval_reference) } else { ch_reference = [] }
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if (params.shortread_hostremoval_index ) { ch_reference_index = file(params.shortread_hostremoval_index ) } else { ch_reference_index = [] }
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -49,6 +52,7 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
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include { DB_CHECK } from '../subworkflows/local/db_check'
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include { SHORTREAD_PREPROCESSING } from '../subworkflows/local/shortread_preprocessing'
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include { LONGREAD_PREPROCESSING } from '../subworkflows/local/longread_preprocessing'
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include { SHORTREAD_HOSTREMOVAL } from '../subworkflows/local/shortread_hostremoval'
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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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@ -121,16 +125,23 @@ workflow TAXPROFILER {
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ch_longreads_preprocessed = LONGREAD_PREPROCESSING ( INPUT_CHECK.out.nanopore ).reads
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.map { it -> [ it[0], [it[1]] ] }
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ch_versions = ch_versions.mix(LONGREAD_PREPROCESSING.out.versions.first())
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} else {
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} else {SHORTREAD_HOSTREMOVAL
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ch_longreads_preprocessed = INPUT_CHECK.out.nanopore
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}
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if ( params.shortread_hostremoval ) {
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ch_shortreads_hostremoved = SHORTREAD_HOSTREMOVAL ( ch_shortreads_preprocessed, ch_reference, ch_reference_index ).reads
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ch_versions = ch_versions.mix(SHORTREAD_HOSTREMOVAL.out.versions.first())
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} else {
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ch_shortreads_hostremoved = ch_shortreads_preprocessed
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}
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/*
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COMBINE READS WITH POSSIBLE DATABASES
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*/
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// e.g. output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
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ch_input_for_profiling = ch_shortreads_preprocessed
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ch_input_for_profiling = ch_shortreads_hostremoved
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.mix( ch_longreads_preprocessed )
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.combine(DB_CHECK.out.dbs)
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.branch {
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@ -196,9 +207,15 @@ workflow TAXPROFILER {
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if (params.shortread_clipmerge) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_PREPROCESSING.out.mqc)
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}
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if (params.shortread_hostremoval) {
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ch_multiqc_files = ch_multiqc_files.mix(SHORTREAD_HOSTREMOVAL.out.mqc.collect{it[1]}.ifEmpty([]))
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}
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if (params.longread_clip) {
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ch_multiqc_files = ch_multiqc_files.mix(LONGREAD_PREPROCESSING.out.mqc)
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}
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if (params.run_kraken2) {
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ch_multiqc_files = ch_multiqc_files.mix(KRAKEN2_KRAKEN2.out.txt.collect{it[1]}.ifEmpty([]))
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ch_versions = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first())
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