Updated bowtie2 (6be004e4) · Commits · Chaos / Cutandrun

modules.json

+1 −1

Original line number	Diff line number	Diff line
		@@ -19,7 +19,7 @@
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"bowtie2/align": {
		"git_sha": "61f68913fefc20241ceccb671b104230b2d775d7"
		"git_sha": "cbc47767f7bb4751a9d178395bd66f051401a0c1"
		},
		"bowtie2/build": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/nf-core/modules/bowtie2/align/main.nf

+49 −59

Original line number	Diff line number	Diff line
		process BOWTIE2_ALIGN {
		tag "$meta.id"
		label 'process_high'
		label "process_high"

		conda (params.enable_conda ? 'bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6' : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' :
		'quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0' }"
		conda (params.enable_conda ? "bioconda::bowtie2=2.4.4 bioconda::samtools=1.15.1 conda-forge::pigz=2.6" : null)
		container "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ?
		"https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" :
		"quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }"

		input:
		tuple val(meta), path(reads)
		path index
		val save_unaligned
		val sort_bam

		output:
		tuple val(meta), path('*.bam') , emit: bam
		tuple val(meta), path('*.log') , emit: log
		tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true
		tuple val(meta), path("*.bam") , emit: bam
		tuple val(meta), path("*.log") , emit: log
		tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true
		path "versions.yml" , emit: versions

		when:
		task.ext.when == null \|\| task.ext.when

		script:
		def args = task.ext.args ?: ''
		def args2 = task.ext.args2 ?: ''
		def args = task.ext.args ?: ""
		def args2 = task.ext.args2 ?: ""
		def prefix = task.ext.prefix ?: "${meta.id}"
		if (meta.single_end) {
		def unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
		"""
		INDEX=`find -L ./ -name "*.rev.1.bt2" \| sed 's/.rev.1.bt2//'`
		[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" \| sed 's/.rev.1.bt2l//'`
		[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
		bowtie2 \\
		-x \$INDEX \\
		-U $reads \\
		--threads $task.cpus \\
		$unaligned \\
		$args \\
		2> ${prefix}.bowtie2.log \\
		\| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -

		cat <<-END_VERSIONS > versions.yml
		"${task.process}":
		bowtie2: \$(echo \$(bowtie2 --version 2>&1) \| sed 's/^.bowtie2-align-s version //; s/ .\$//')
		samtools: \$(echo \$(samtools --version 2>&1) \| sed 's/^.samtools //; s/Using.\$//')
		pigz: \$( pigz --version 2>&1 \| sed 's/pigz //g' )
		END_VERSIONS
		"""
		def unaligned = ""
		def reads_args = ""
		if (meta.single_end) {
		unaligned = save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ""
		reads_args = "-U ${reads}"
		} else {
		def unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
		unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ""
		reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
		}

		def samtools_command = sort_bam ? 'sort' : 'view'

		"""
		INDEX=`find -L ./ -name "*.rev.1.bt2" \| sed 's/.rev.1.bt2//'`
		[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" \| sed 's/.rev.1.bt2l//'`
		[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
		INDEX=`find -L ./ -name "*.rev.1.bt2" \| sed "s/.rev.1.bt2//"`
		[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" \| sed "s/.rev.1.bt2l//"`
		[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1

		bowtie2 \\
		-x \$INDEX \\
		-1 ${reads[0]} \\
		-2 ${reads[1]} \\
		$reads_args \\
		--threads $task.cpus \\
		$unaligned \\
		$args \\
		2> ${prefix}.bowtie2.log \\
		\| samtools view -@ $task.cpus $args2 -bhS -o ${prefix}.bam -
		\| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -

		if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
		mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
		fi

		if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
		mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
		fi
		@@ -78,4 +69,3 @@ process BOWTIE2_ALIGN {
		END_VERSIONS
		"""
		}
		}

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