Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/modules/cat/unique/main.nf @ 6:a3c1cba6f773
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 19:52:20 -0500 |
| parents | c8597e9e1a97 |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process CAT_UNIQUE { |
| kkonganti@0 | 2 tag "${meta.id}" |
| kkonganti@0 | 3 label "process_pico" |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "conda-forge::perl conda-forge::coreutils bioconda::perl-bioperl=1.7.8" : null) |
| kkonganti@0 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@0 | 8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' : |
| kkonganti@0 | 9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" |
| kkonganti@0 | 10 |
| kkonganti@0 | 11 input: |
| kkonganti@0 | 12 tuple val(meta), path(file) |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 output: |
| kkonganti@0 | 15 path '*_uniq.txt' , emit: txt |
| kkonganti@0 | 16 path 'versions.yml', emit: versions |
| kkonganti@0 | 17 |
| kkonganti@0 | 18 when: |
| kkonganti@0 | 19 task.ext.when == null || task.ext.when |
| kkonganti@0 | 20 |
| kkonganti@0 | 21 script: |
| kkonganti@0 | 22 def args = (task.ext.args ?: '') |
| kkonganti@0 | 23 def skip = (meta.skip_header ?: 1) |
| kkonganti@0 | 24 prefix = (task.ext.prefix ?: meta.id) |
| kkonganti@0 | 25 """ |
| kkonganti@0 | 26 newfile=\$(echo "$file" | sed -e 's/_w_dups/_uniq/g') |
| kkonganti@0 | 27 |
| kkonganti@0 | 28 head -n$skip "$file" > \$newfile |
| kkonganti@0 | 29 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> \$newfile |
| kkonganti@0 | 30 |
| kkonganti@0 | 31 uniqver="" |
| kkonganti@0 | 32 |
| kkonganti@0 | 33 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@0 | 34 uniqver=\$( uniq --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@0 | 35 |
| kkonganti@0 | 36 else |
| kkonganti@0 | 37 uniqver=\$( uniq --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@0 | 38 fi |
| kkonganti@0 | 39 |
| kkonganti@0 | 40 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 41 "${task.process}": |
| kkonganti@0 | 42 head: \$uniqver |
| kkonganti@0 | 43 tail: \$uniqver |
| kkonganti@0 | 44 sort: \$uniqver |
| kkonganti@0 | 45 uniq: \$uniqver |
| kkonganti@0 | 46 END_VERSIONS |
| kkonganti@0 | 47 """ |
| kkonganti@0 | 48 } |