Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.0/modules/seqkit/rmdup/main.nf @ 101:ce6d9548fe89
"planemo upload"
| author | kkonganti |
|---|---|
| date | Thu, 04 Aug 2022 10:45:55 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@101 | 1 process SEQKIT_RMDUP { |
| kkonganti@101 | 2 tag "$meta.id" |
| kkonganti@101 | 3 label 'process_low' |
| kkonganti@101 | 4 |
| kkonganti@101 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null) |
| kkonganti@101 | 6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) |
| kkonganti@101 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@101 | 8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': |
| kkonganti@101 | 9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" |
| kkonganti@101 | 10 |
| kkonganti@101 | 11 input: |
| kkonganti@101 | 12 tuple val(meta), path(reads) |
| kkonganti@101 | 13 |
| kkonganti@101 | 14 output: |
| kkonganti@101 | 15 tuple val(meta), path("*duplicated.details.txt"), optional: true |
| kkonganti@101 | 16 tuple val(meta), path("*.gz") , emit: fastx |
| kkonganti@101 | 17 path "versions.yml" , emit: versions |
| kkonganti@101 | 18 |
| kkonganti@101 | 19 when: |
| kkonganti@101 | 20 task.ext.when == null || task.ext.when |
| kkonganti@101 | 21 |
| kkonganti@101 | 22 script: |
| kkonganti@101 | 23 def args = task.ext.args ?: '' |
| kkonganti@101 | 24 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@101 | 25 def rmdup_d = params.seqkit_rmdup_d ? "-d ${prefix}.seqs.duplicated.fastq.gz" : "" |
| kkonganti@101 | 26 def rmdup_D = params.seqkit_rmdup_D ? "-D ${prefix}.duplicated.details.txt" : "" |
| kkonganti@101 | 27 |
| kkonganti@101 | 28 def extension = "fastq" |
| kkonganti@101 | 29 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { |
| kkonganti@101 | 30 extension = "fasta" |
| kkonganti@101 | 31 } |
| kkonganti@101 | 32 |
| kkonganti@101 | 33 if (meta.single_end) { |
| kkonganti@101 | 34 """ |
| kkonganti@101 | 35 seqkit \\ |
| kkonganti@101 | 36 rmdup \\ |
| kkonganti@101 | 37 $rmdup_d \\ |
| kkonganti@101 | 38 $rmdup_D \\ |
| kkonganti@101 | 39 -j $task.cpus \\ |
| kkonganti@101 | 40 -o ${prefix}.seqkit-rmdup.${extension}.gz \\ |
| kkonganti@101 | 41 $args \\ |
| kkonganti@101 | 42 $reads |
| kkonganti@101 | 43 |
| kkonganti@101 | 44 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 45 "${task.process}": |
| kkonganti@101 | 46 seqkit: \$( seqkit | sed '3!d; s/Version: //' ) |
| kkonganti@101 | 47 END_VERSIONS |
| kkonganti@101 | 48 """ |
| kkonganti@101 | 49 } else { |
| kkonganti@101 | 50 """ |
| kkonganti@101 | 51 seqkit \\ |
| kkonganti@101 | 52 rmdup \\ |
| kkonganti@101 | 53 $rmdup_d \\ |
| kkonganti@101 | 54 $rmdup_D \\ |
| kkonganti@101 | 55 -j $task.cpus \\ |
| kkonganti@101 | 56 -o ${prefix}.R1.seqkit-rmdup.${extension}.gz \\ |
| kkonganti@101 | 57 $args \\ |
| kkonganti@101 | 58 ${reads[0]} |
| kkonganti@101 | 59 |
| kkonganti@101 | 60 seqkit \\ |
| kkonganti@101 | 61 rmdup \\ |
| kkonganti@101 | 62 $rmdup_d \\ |
| kkonganti@101 | 63 $rmdup_D \\ |
| kkonganti@101 | 64 -j $task.cpus \\ |
| kkonganti@101 | 65 -o ${prefix}.R2.seqkit-rmdup.${extension}.gz \\ |
| kkonganti@101 | 66 $args \\ |
| kkonganti@101 | 67 ${reads[1]} |
| kkonganti@101 | 68 |
| kkonganti@101 | 69 seqkit \\ |
| kkonganti@101 | 70 pair \\ |
| kkonganti@101 | 71 -j $task.cpus \\ |
| kkonganti@101 | 72 -1 ${prefix}.R1.seqkit-rmdup.${extension}.gz \\ |
| kkonganti@101 | 73 -2 ${prefix}.R2.seqkit-rmdup.${extension}.gz |
| kkonganti@101 | 74 |
| kkonganti@101 | 75 rm ${prefix}.R1.seqkit-rmdup.${extension}.gz |
| kkonganti@101 | 76 rm ${prefix}.R2.seqkit-rmdup.${extension}.gz |
| kkonganti@101 | 77 |
| kkonganti@101 | 78 cat <<-END_VERSIONS > versions.yml |
| kkonganti@101 | 79 "${task.process}": |
| kkonganti@101 | 80 seqkit: \$( seqkit | sed '3!d; s/Version: //' ) |
| kkonganti@101 | 81 END_VERSIONS |
| kkonganti@101 | 82 """ |
| kkonganti@101 | 83 } |
| kkonganti@101 | 84 } |