Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.1.0/modules/scaffold_genomes/main.nf @ 0:c8597e9e1a97
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 27 Nov 2023 12:37:44 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@0 | 1 process SCAFFOLD_GENOMES { |
| kkonganti@0 | 2 tag "fasta_join.pl" |
| kkonganti@0 | 3 label "process_micro" |
| kkonganti@0 | 4 |
| kkonganti@0 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null) |
| kkonganti@0 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null) |
| kkonganti@0 | 7 container "${ 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 path acc_chunk_file |
| kkonganti@0 | 13 |
| kkonganti@0 | 14 output: |
| kkonganti@0 | 15 val "${params.output}${params.fs}scaffold_genomes", emit: genomes_dir |
| kkonganti@0 | 16 path '*_scaffolded_genomic.fna.gz' , emit: scaffolded |
| kkonganti@0 | 17 path 'versions.yml' , emit: versions |
| kkonganti@0 | 18 |
| kkonganti@0 | 19 when: |
| kkonganti@0 | 20 task.ext.when == null || task.ext.when |
| kkonganti@0 | 21 |
| kkonganti@0 | 22 script: |
| kkonganti@0 | 23 def args = task.ext.args ?: '' |
| kkonganti@0 | 24 """ |
| kkonganti@0 | 25 datasets download genome accession \\ |
| kkonganti@0 | 26 --dehydrated \\ |
| kkonganti@0 | 27 --inputfile $acc_chunk_file |
| kkonganti@0 | 28 |
| kkonganti@0 | 29 unzip ncbi_dataset.zip |
| kkonganti@0 | 30 |
| kkonganti@0 | 31 datasets rehydrate \\ |
| kkonganti@0 | 32 --gzip \\ |
| kkonganti@0 | 33 --max-workers $task.cpus \\ |
| kkonganti@0 | 34 --directory "." |
| kkonganti@0 | 35 |
| kkonganti@0 | 36 fasta_join.pl -in ncbi_dataset |
| kkonganti@0 | 37 |
| kkonganti@0 | 38 cat <<-END_VERSIONS > versions.yml |
| kkonganti@0 | 39 "${task.process}": |
| kkonganti@0 | 40 datasets: \$( datasets --version | sed 's/datasets version: //g' ) |
| kkonganti@0 | 41 perl: \$( perl -e 'print \$^V' | sed 's/v//g' ) |
| kkonganti@0 | 42 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION') |
| kkonganti@0 | 43 END_VERSIONS |
| kkonganti@0 | 44 |
| kkonganti@0 | 45 zcmd="" |
| kkonganti@0 | 46 zver="" |
| kkonganti@0 | 47 |
| kkonganti@0 | 48 if type pigz > /dev/null 2>&1; then |
| kkonganti@0 | 49 zcmd="pigz" |
| kkonganti@0 | 50 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" ) |
| kkonganti@0 | 51 elif type gzip > /dev/null 2>&1; then |
| kkonganti@0 | 52 zcmd="gzip" |
| kkonganti@0 | 53 |
| kkonganti@0 | 54 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@0 | 55 zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@0 | 56 else |
| kkonganti@0 | 57 zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" ) |
| kkonganti@0 | 58 fi |
| kkonganti@0 | 59 fi |
| kkonganti@0 | 60 |
| kkonganti@0 | 61 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@0 | 62 \$zcmd: \$zver |
| kkonganti@0 | 63 END_VERSIONS |
| kkonganti@0 | 64 """ |
| kkonganti@0 | 65 } |