diff --git a/modules/bowtie2/align/main.nf b/modules/bowtie2/align/main.nf index c233f955..38242fcb 100644 --- a/modules/bowtie2/align/main.nf +++ b/modules/bowtie2/align/main.nf @@ -1,11 +1,11 @@ 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 "${ workflow.containerEngine == "singularity" && !task.ext.singularity_pull_docker_container ? + "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" : + "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:1744f68fe955578c63054b55309e05b41c37a80d-0" }" input: tuple val(meta), path(reads) @@ -13,69 +13,60 @@ process BOWTIE2_ALIGN { val save_unaligned output: - tuple val(meta), path('*.bam') , emit: bam - tuple val(meta), path('*.log') , emit: log - tuple val(meta), path('*fastq.gz'), emit: fastq, optional:true + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.log") , emit: log + tuple val(meta), path("*fastq.gz"), emit: fastq, optional:true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def args2 = task.ext.args2 ?: '' + def args = task.ext.args ?: "" + def args2 = task.ext.args2 ?: "" def prefix = task.ext.prefix ?: "${meta.id}" + + def unaligned = "" + def reads_args = "" 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 - """ + 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" : '' - """ - 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 \\ - -1 ${reads[0]} \\ - -2 ${reads[1]} \\ - --threads $task.cpus \\ - $unaligned \\ - $args \\ - 2> ${prefix}.bowtie2.log \\ - | samtools view -@ $task.cpus $args2 -bhS -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 ${prefix}.unmapped_2.fastq.gz - fi - - cat <<-END_VERSIONS > versions.yml - "${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 - """ + unaligned = save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : "" + reads_args = "-1 ${reads[0]} -2 ${reads[1]}" } + + def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam" + + + """ + 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 \\ + $reads_args \\ + --threads $task.cpus \\ + $unaligned \\ + $args \\ + 2> ${prefix}.bowtie2.log \\ + | $samtools_command + + 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 ${prefix}.unmapped_2.fastq.gz + fi + + cat <<-END_VERSIONS > versions.yml + "${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 + """ } + diff --git a/tests/modules/bowtie2/align/test.yml b/tests/modules/bowtie2/align/test.yml index ea9aa72a..ef05d70d 100644 --- a/tests/modules/bowtie2/align/test.yml +++ b/tests/modules/bowtie2/align/test.yml @@ -1,83 +1,21 @@ -- name: bowtie2 align single-end +- name: bowtie2 align test_bowtie2_align_single_end command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2 - bowtie2/align + - bowtie2 files: - - path: ./output/bowtie2/test.bam - - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/bowtie2/bowtie2/genome.3.bt2 - md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/bowtie2/bowtie2/genome.2.bt2 - md5sum: 47b153cd1319abc88dda532462651fcf - - path: ./output/bowtie2/bowtie2/genome.1.bt2 - md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf - - path: ./output/bowtie2/bowtie2/genome.4.bt2 - md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2 - md5sum: 52be6950579598a990570fbcf5372184 - - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2 - md5sum: e3b4ef343dea4dd571642010a7d09597 + - path: output/bowtie2/test.bam + - path: output/bowtie2/test.bowtie2.log + md5sum: 7b8a9e61b7646da1089b041333c41a87 + - path: output/bowtie2/versions.yml -- name: bowtie2 align paired-end +- name: bowtie2 align test_bowtie2_align_paired_end command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config tags: - - bowtie2 - bowtie2/align - files: - - path: ./output/bowtie2/test.bam - - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/bowtie2/bowtie2/genome.3.bt2 - md5sum: 4ed93abba181d8dfab2e303e33114777 - - path: ./output/bowtie2/bowtie2/genome.2.bt2 - md5sum: 47b153cd1319abc88dda532462651fcf - - path: ./output/bowtie2/bowtie2/genome.1.bt2 - md5sum: cbe3d0bbea55bc57c99b4bfa25b5fbdf - - path: ./output/bowtie2/bowtie2/genome.4.bt2 - md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2 - md5sum: 52be6950579598a990570fbcf5372184 - - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2 - md5sum: e3b4ef343dea4dd571642010a7d09597 - -- name: bowtie2 align single-end large-index - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index - tags: - bowtie2 - - bowtie2/align files: - - path: ./output/bowtie2/test.bam - - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/bowtie2/bowtie2/genome.3.bt2l - md5sum: 8952b3e0b1ce9a7a5916f2e147180853 - - path: ./output/bowtie2/bowtie2/genome.2.bt2l - md5sum: 22c284084784a0720989595e0c9461fd - - path: ./output/bowtie2/bowtie2/genome.1.bt2l - md5sum: 07d811cd4e350d56267183d2ac7023a5 - - path: ./output/bowtie2/bowtie2/genome.4.bt2l - md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l - md5sum: fda48e35925fb24d1c0785f021981e25 - - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l - md5sum: 802c26d32b970e1b105032b7ce7348b4 - -- name: bowtie2 align paired-end large-index - command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config --force_large_index - tags: - - bowtie2 - - bowtie2/align - files: - - path: ./output/bowtie2/test.bam - - path: ./output/bowtie2/test.bowtie2.log - - path: ./output/bowtie2/bowtie2/genome.3.bt2l - md5sum: 8952b3e0b1ce9a7a5916f2e147180853 - - path: ./output/bowtie2/bowtie2/genome.2.bt2l - md5sum: 22c284084784a0720989595e0c9461fd - - path: ./output/bowtie2/bowtie2/genome.1.bt2l - md5sum: 07d811cd4e350d56267183d2ac7023a5 - - path: ./output/bowtie2/bowtie2/genome.4.bt2l - md5sum: c25be5f8b0378abf7a58c8a880b87626 - - path: ./output/bowtie2/bowtie2/genome.rev.1.bt2l - md5sum: fda48e35925fb24d1c0785f021981e25 - - path: ./output/bowtie2/bowtie2/genome.rev.2.bt2l - md5sum: 802c26d32b970e1b105032b7ce7348b4 + - path: output/bowtie2/test.bam + - path: output/bowtie2/test.bowtie2.log + md5sum: bd89ce1b28c93bf822bae391ffcedd19 + - path: output/bowtie2/versions.yml