Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/scaffold_genomes/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 process SCAFFOLD_GENOMES { |
| kkonganti@1 | 2 tag "fasta_join.pl" |
| kkonganti@1 | 3 label "process_nano" |
| kkonganti@1 | 4 |
| kkonganti@1 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null) |
| kkonganti@1 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null) |
| kkonganti@1 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@1 | 8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' : |
| kkonganti@1 | 9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 input: |
| kkonganti@1 | 12 path acc_chunk_file |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 output: |
| kkonganti@1 | 15 val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir |
| kkonganti@1 | 16 path '*_scaffolded_genomic.fna.gz' , emit: scaffolded |
| kkonganti@1 | 17 path 'versions.yml' , emit: versions |
| kkonganti@1 | 18 |
| kkonganti@1 | 19 when: |
| kkonganti@1 | 20 task.ext.when == null || task.ext.when |
| kkonganti@1 | 21 |
| kkonganti@1 | 22 script: |
| kkonganti@1 | 23 def args = task.ext.args ?: '' |
| kkonganti@1 | 24 """ |
| kkonganti@1 | 25 datasets download genome accession \\ |
| kkonganti@1 | 26 --dehydrated \\ |
| kkonganti@1 | 27 --inputfile $acc_chunk_file |
| kkonganti@1 | 28 |
| kkonganti@1 | 29 unzip ncbi_dataset.zip |
| kkonganti@1 | 30 |
| kkonganti@1 | 31 datasets rehydrate \\ |
| kkonganti@1 | 32 --gzip \\ |
| kkonganti@1 | 33 --directory "." |
| kkonganti@1 | 34 |
| kkonganti@1 | 35 fasta_join.pl -in ncbi_dataset |
| kkonganti@1 | 36 |
| kkonganti@1 | 37 cat <<-END_VERSIONS > versions.yml |
| kkonganti@1 | 38 "${task.process}": |
| kkonganti@1 | 39 datasets: \$( datasets --version | sed 's/datasets version: //g' ) |
| kkonganti@1 | 40 perl: \$( perl -e 'print \$^V' | sed 's/v//g' ) |
| kkonganti@1 | 41 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION') |
| kkonganti@1 | 42 END_VERSIONS |
| kkonganti@1 | 43 |
| kkonganti@1 | 44 zcmd="" |
| kkonganti@1 | 45 zver="" |
| kkonganti@1 | 46 |
| kkonganti@1 | 47 if type pigz > /dev/null 2>&1; then |
| kkonganti@1 | 48 zcmd="pigz" |
| kkonganti@1 | 49 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) |
| kkonganti@1 | 50 elif type gzip > /dev/null 2>&1; then |
| kkonganti@1 | 51 zcmd="gzip" |
| kkonganti@1 | 52 |
| kkonganti@1 | 53 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@1 | 54 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@1 | 55 else |
| kkonganti@1 | 56 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) |
| kkonganti@1 | 57 fi |
| kkonganti@1 | 58 fi |
| kkonganti@1 | 59 |
| kkonganti@1 | 60 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@1 | 61 \$zcmd: \$zver |
| kkonganti@1 | 62 END_VERSIONS |
| kkonganti@1 | 63 """ |
| kkonganti@1 | 64 } |