Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/db_per_snp_cluster/main.nf @ 21:4ce0e079377d tip
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 12:01:00 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 process DB_PER_SNP_CLUSTER { |
| kkonganti@17 | 2 tag "waterfall_per_snp_cluster.pl" |
| kkonganti@17 | 3 label "process_pico" |
| kkonganti@17 | 4 |
| kkonganti@17 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null) |
| kkonganti@17 | 6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null) |
| kkonganti@17 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@17 | 8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' : |
| kkonganti@17 | 9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 input: |
| kkonganti@17 | 12 path accs_tbl |
| kkonganti@17 | 13 path pdg_metadata |
| kkonganti@17 | 14 path snp_cluster_metadata |
| kkonganti@17 | 15 |
| kkonganti@17 | 16 output: |
| kkonganti@17 | 17 path '*asm_chunk_snp.tbl' , emit: asm_chunk_snp_tbl |
| kkonganti@17 | 18 path '*asm_chunk_snp_counts.tbl', emit: asm_chunk_snp_counts |
| kkonganti@17 | 19 path '*accs_snp.txt' , emit: accs_snp |
| kkonganti@17 | 20 path 'mash_snp_genome_list.txt' , emit: genome_paths |
| kkonganti@17 | 21 path 'versions.yml' , emit: versions |
| kkonganti@17 | 22 |
| kkonganti@17 | 23 when: |
| kkonganti@17 | 24 task.ext.when == null || task.ext.when |
| kkonganti@17 | 25 |
| kkonganti@17 | 26 script: |
| kkonganti@17 | 27 def args = task.ext.args ?: '' |
| kkonganti@17 | 28 def prefix = task.index ?: '' |
| kkonganti@17 | 29 """ |
| kkonganti@17 | 30 waterfall_per_snp_cluster.pl \\ |
| kkonganti@17 | 31 -p $pdg_metadata \\ |
| kkonganti@17 | 32 -tb $accs_tbl \\ |
| kkonganti@17 | 33 -snp $snp_cluster_metadata \\ |
| kkonganti@17 | 34 $args \\ |
| kkonganti@17 | 35 1> asm_chunk_snp.tbl 2> asm_chunk_snp_counts.tbl |
| kkonganti@17 | 36 |
| kkonganti@17 | 37 cat <<-END_VERSIONS > versions.yml |
| kkonganti@17 | 38 "${task.process}": |
| kkonganti@17 | 39 perl: \$( perl -e 'print \$^V' | sed 's/v//g' ) |
| kkonganti@17 | 40 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION') |
| kkonganti@17 | 41 END_VERSIONS |
| kkonganti@17 | 42 """ |
| kkonganti@17 | 43 } |