Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/seqkit/seq/main.nf @ 130:04f6ac8ca13c
planemo upload
| author | kkonganti |
|---|---|
| date | Wed, 03 Jul 2024 15:16:39 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process SEQKIT_SEQ { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_low' |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqkit${params.fs}2.2.0" : null) |
| kkonganti@105 | 6 conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null) |
| kkonganti@105 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 8 'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0': |
| kkonganti@105 | 9 'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }" |
| kkonganti@105 | 10 |
| kkonganti@105 | 11 input: |
| kkonganti@105 | 12 tuple val(meta), path(reads) |
| kkonganti@105 | 13 |
| kkonganti@105 | 14 output: |
| kkonganti@105 | 15 tuple val(meta), path("*.gz"), emit: fastx |
| kkonganti@105 | 16 path "versions.yml" , emit: versions |
| kkonganti@105 | 17 |
| kkonganti@105 | 18 when: |
| kkonganti@105 | 19 task.ext.when == null || task.ext.when |
| kkonganti@105 | 20 |
| kkonganti@105 | 21 script: |
| kkonganti@105 | 22 def args = task.ext.args ?: '' |
| kkonganti@105 | 23 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@105 | 24 |
| kkonganti@105 | 25 def extension = "fastq" |
| kkonganti@105 | 26 if ("$reads" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/) { |
| kkonganti@105 | 27 extension = "fasta" |
| kkonganti@105 | 28 } |
| kkonganti@105 | 29 |
| kkonganti@105 | 30 if (meta.single_end) { |
| kkonganti@105 | 31 """ |
| kkonganti@105 | 32 seqkit \\ |
| kkonganti@105 | 33 seq \\ |
| kkonganti@105 | 34 -j $task.cpus \\ |
| kkonganti@105 | 35 -o ${prefix}.seqkit-seq.${extension}.gz \\ |
| kkonganti@105 | 36 $args \\ |
| kkonganti@105 | 37 $reads |
| kkonganti@105 | 38 |
| kkonganti@105 | 39 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 40 "${task.process}": |
| kkonganti@105 | 41 seqkit: \$( seqkit | sed '3!d; s/Version: //' ) |
| kkonganti@105 | 42 END_VERSIONS |
| kkonganti@105 | 43 """ |
| kkonganti@105 | 44 } else { |
| kkonganti@105 | 45 """ |
| kkonganti@105 | 46 seqkit \\ |
| kkonganti@105 | 47 seq \\ |
| kkonganti@105 | 48 -j $task.cpus \\ |
| kkonganti@105 | 49 -o ${prefix}.R1.seqkit-seq.${extension}.gz \\ |
| kkonganti@105 | 50 $args \\ |
| kkonganti@105 | 51 ${reads[0]} |
| kkonganti@105 | 52 |
| kkonganti@105 | 53 seqkit \\ |
| kkonganti@105 | 54 seq \\ |
| kkonganti@105 | 55 -j $task.cpus \\ |
| kkonganti@105 | 56 -o ${prefix}.R2.seqkit-seq.${extension}.gz \\ |
| kkonganti@105 | 57 $args \\ |
| kkonganti@105 | 58 ${reads[1]} |
| kkonganti@105 | 59 |
| kkonganti@105 | 60 seqkit \\ |
| kkonganti@105 | 61 pair \\ |
| kkonganti@105 | 62 -j $task.cpus \\ |
| kkonganti@105 | 63 -1 ${prefix}.R1.seqkit-seq.${extension}.gz \\ |
| kkonganti@105 | 64 -2 ${prefix}.R2.seqkit-seq.${extension}.gz |
| kkonganti@105 | 65 |
| kkonganti@105 | 66 rm ${prefix}.R1.seqkit-seq.${extension}.gz |
| kkonganti@105 | 67 rm ${prefix}.R2.seqkit-seq.${extension}.gz |
| kkonganti@105 | 68 |
| kkonganti@105 | 69 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 70 "${task.process}": |
| kkonganti@105 | 71 seqkit: \$( seqkit | sed '3!d; s/Version: //' ) |
| kkonganti@105 | 72 END_VERSIONS |
| kkonganti@105 | 73 """ |
| kkonganti@105 | 74 } |
| kkonganti@105 | 75 } |