process CNVKIT_BATCH { tag "$meta.id" label 'process_low' conda (params.enable_conda ? 'bioconda::cnvkit=0.9.9 bioconda::samtools=1.15.1' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' : 'quay.io/biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:304d1c5ab610f216e77c61420ebe85f1e7c5968a-0' }" input: tuple val(meta), path(tumor), path(normal) path fasta path fasta_fai path targets path reference output: tuple val(meta), path("*.bed"), emit: bed tuple val(meta), path("*.cnn"), emit: cnn, optional: true tuple val(meta), path("*.cnr"), emit: cnr, optional: true tuple val(meta), path("*.cns"), emit: cns, optional: true tuple val(meta), path("*.pdf"), emit: pdf, optional: true tuple val(meta), path("*.png"), emit: png, optional: true path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def tumor_exists = tumor ? true : false def normal_exists = normal ? true : false // execute samtools only when cram files are input, cnvkit runs natively on bam but is prohibitively slow def tumor_cram = tumor_exists && tumor.Extension == "cram" ? true : false def normal_cram = normal_exists && normal.Extension == "cram" ? true : false def tumor_bam = tumor_exists && tumor.Extension == "bam" ? true : false def normal_bam = normal_exists && normal.Extension == "bam" ? true : false def tumor_out = tumor_cram ? tumor.BaseName + ".bam" : "${tumor}" // tumor_only mode does not need fasta & target // instead it requires a pre-computed reference.cnn which is built from fasta & target def (normal_out, normal_args, fasta_args) = ["", "", ""] def fai_reference = fasta_fai ? "--fai-reference ${fasta_fai}" : "" if (normal_exists){ def normal_prefix = normal.BaseName normal_out = normal_cram ? "${normal_prefix}" + ".bam" : "${normal}" fasta_args = fasta ? "--fasta $fasta" : "" // germline mode // normal samples must be input without a flag // requires flag --normal to be empty [] if(!tumor_exists){ tumor_out = "${normal_prefix}" + ".bam" normal_args = "--normal " } // somatic mode else { normal_args = normal_prefix ? "--normal $normal_out" : "" } } def target_args = targets ? "--targets $targets" : "" def reference_args = reference ? "--reference $reference" : "" // somatic_mode cram_input if (tumor_cram && normal_cram){ """ samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $normal_out cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } // somatic_mode bam_input else if (tumor_bam && normal_bam){ """ cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } // tumor_only_mode cram_input else if(tumor_cram && !normal_exists){ """ samtools view -T $fasta $fai_reference $tumor -@ $task.cpus -o $tumor_out cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } // tumor_only bam_input else if(tumor_bam && !normal_exists){ """ cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } // germline mode cram_input // normal_args must be --normal [] else if (normal_cram && !tumor_exists){ """ samtools view -T $fasta $fai_reference $normal -@ $task.cpus -o $tumor_out cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } // germline mode bam_input else if (normal_bam && !tumor_exists){ """ cnvkit.py \\ batch \\ $tumor_out \\ $normal_args \\ $fasta_args \\ $reference_args \\ $target_args \\ --processes $task.cpus \\ $args cat <<-END_VERSIONS > versions.yml "${task.process}": cnvkit: \$(cnvkit.py version | sed -e "s/cnvkit v//g") END_VERSIONS """ } }