Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/cat/unique/main.nf @ 14:9e80528263c4
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 17:32:05 -0400 |
| parents | a5f31c44f8c9 |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process CAT_UNIQUE { |
| kkonganti@11 | 2 tag "${meta.id}" |
| kkonganti@11 | 3 label "process_pico" |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "conda-forge::perl conda-forge::coreutils bioconda::perl-bioperl=1.7.8" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' : |
| kkonganti@11 | 9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(file) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 path '*_uniq.txt' , emit: txt |
| kkonganti@11 | 16 path '*metadata.csv', emit: csv, optional: true |
| kkonganti@11 | 17 path 'versions.yml' , emit: versions |
| kkonganti@11 | 18 |
| kkonganti@11 | 19 when: |
| kkonganti@11 | 20 task.ext.when == null || task.ext.when |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 script: |
| kkonganti@11 | 23 def args = (task.ext.args ?: '') |
| kkonganti@11 | 24 def skip = (meta.skip_header ?: 1) |
| kkonganti@11 | 25 prefix = (task.ext.prefix ?: meta.id) |
| kkonganti@11 | 26 """ |
| kkonganti@11 | 27 newfile=\$(echo "$file" | sed -e 's/_w_dups/_uniq/g') |
| kkonganti@11 | 28 |
| kkonganti@11 | 29 head -n$skip "$file" > \$newfile |
| kkonganti@11 | 30 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> \$newfile |
| kkonganti@11 | 31 |
| kkonganti@11 | 32 if [ "\$newfile" == "iTOL_metadata_uniq.txt" ]; then |
| kkonganti@11 | 33 head -n3 "$file" | tail -n1 | sed -e 's/^FIELD_LABELS/ID/' > microreact_metadata.csv |
| kkonganti@11 | 34 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> microreact_metadata.csv |
| kkonganti@11 | 35 fi |
| kkonganti@11 | 36 |
| kkonganti@11 | 37 uniqver="" |
| kkonganti@11 | 38 |
| kkonganti@11 | 39 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@11 | 40 uniqver=\$( uniq --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@11 | 41 |
| kkonganti@11 | 42 else |
| kkonganti@11 | 43 uniqver=\$( uniq --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@11 | 44 fi |
| kkonganti@11 | 45 |
| kkonganti@11 | 46 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 47 "${task.process}": |
| kkonganti@11 | 48 head: \$uniqver |
| kkonganti@11 | 49 tail: \$uniqver |
| kkonganti@11 | 50 sort: \$uniqver |
| kkonganti@11 | 51 uniq: \$uniqver |
| kkonganti@11 | 52 END_VERSIONS |
| kkonganti@11 | 53 """ |
| kkonganti@11 | 54 } |