mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-20 23:32:05 +00:00
1d668eefa2
* Update seqwish to version 0.7.2 * seqwish can work with a comma-separated list of PAFs * level with nf-core/modules master branch * update seqwish/induce to v0.7.6 * add pangenome test data * test seqwish/induce v0.7.6 with pangenomics test data * we already have pointed to the pangenomics test data sets * update paths to test data * add path to bgzipped fa, gzi, fai * remove one tab * remove one tab * actually execute the 2nd test * try to fix versions.yml * pangenomic tests can be run in their own subworkflow * maybe the csv input is the problem * remove space as suggested by Rike * csv input was not the problem * update test.yml * typo * enable pangenome tests * add md5sum for pangenomic test * Update tests/modules/seqwish/induce/test.yml Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> * PAF input is a list of files * beautify comment Co-authored-by: Michael L Heuer <heuermh@acm.org> Co-authored-by: Gisela Gabernet <gisela.gabernet@gmail.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
43 lines
1.4 KiB
Text
43 lines
1.4 KiB
Text
process SEQWISH_INDUCE {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? 'bioconda::seqwish=0.7.6' : null)
|
|
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/seqwish:0.7.6--h5b5514e_1' :
|
|
'quay.io/biocontainers/seqwish:0.7.6--h5b5514e_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(paf), path(fasta)
|
|
|
|
output:
|
|
tuple val(meta), path("*.gfa"), emit: gfa
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def input = paf.join(',') // this ensures that we can actually input a
|
|
// comma-separated list of PAF files as required by
|
|
// https://github.com/nf-core/pangenome. If one wants to use this,
|
|
// ensure that you put a ".collect()" behind your channel.
|
|
// See https://github.com/nf-core/pangenome/blob/34149c6cdc19bce3a7b99f97c769d8986a8d429b/main.nf#L543
|
|
// for an example.
|
|
"""
|
|
seqwish \\
|
|
--threads $task.cpus \\
|
|
--paf-alns=$input \\
|
|
--seqs=$fasta \\
|
|
--gfa=${prefix}.gfa \\
|
|
$args
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
seqwish: \$(echo \$(seqwish --version 2>&1) | cut -f 1 -d '-' | cut -f 2 -d 'v')
|
|
END_VERSIONS
|
|
"""
|
|
}
|