Mercurial > repos > kkonganti > cfsan_bettercallsal

comparison 0.5.0/modules/db_per_snp_cluster/main.nf @ 1:365849f031fd

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"planemo upload"
author kkonganti
date Mon, 05 Jun 2023 18:48:51 -0400
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0:a4b1ee4b68b1 1:365849f031fd
1 process DB_PER_SNP_CLUSTER {
2 tag "waterfall_per_snp_cluster.pl"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
6 conda (params.enable_conda ? "conda-forge::perl bioconda::perl-bioperl=1.7.8" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
10
11 input:
12 path accs_tbl
13 path pdg_metadata
14 path snp_cluster_metadata
15
16 output:
17 path '*asm_chunk_snp.tbl' , emit: asm_chunk_snp_tbl
18 path '*asm_chunk_snp_counts.tbl', emit: asm_chunk_snp_counts
19 path '*accs_snp.txt' , emit: accs_snp
20 path 'mash_snp_genome_list.txt' , emit: genome_paths
21 path 'versions.yml' , emit: versions
22
23 when:
24 task.ext.when == null || task.ext.when
25
26 script:
27 def args = task.ext.args ?: ''
28 def prefix = task.index ?: ''
29 """
30 waterfall_per_snp_cluster.pl \\
31 -p $pdg_metadata \\
32 -t $accs_tbl \\
33 -snp $snp_cluster_metadata \\
34 $args \\
35 1> asm_chunk_snp.tbl 2> asm_chunk_snp_counts.tbl
36
37 cat <<-END_VERSIONS > versions.yml
38 "${task.process}":
39 perl: \$( perl -e 'print \$^V' | sed 's/v//g' )
40 bioperl: \$(perl -MBio::Root::Version -e 'print \$Bio::Root::Version::VERSION')
41 END_VERSIONS
42 """
43 }