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comparison 0.5.0/modules/bcs_distance_matrix/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 BCS_DISTANCE_MATRIX {
2 tag "Samples vs Genomes"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' :
9 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }"
10
11 input:
12 path matrix
13 path labels
14
15 output:
16 path 'bcs_sourmash_matrix.tblsum.txt', emit: mqc_txt, optional: true
17 path 'bcs_sourmash_matrix_mqc.json' , emit: mqc_json, optional: true
18 path 'bcs_sourmash_matrix_mqc.yml' , emit: mqc_yml, optional: true
19 path 'versions.yml' , emit: versions
20
21 when:
22 task.ext.when == null || task.ext.when
23
24 script:
25 def args = task.ext.args ?: ''
26
27 """
28 sourmash_sim_matrix.py \\
29 -pickle ${params.tuspy_ps} \\
30 -csv $matrix \\
31 -labels $labels
32
33 if [ -e "bcs_sourmash_matrix.tblsum.txt" ] && [ -s "bcs_sourmash_matrix.tblsum.txt" ]; then
34 create_mqc_data_table.py \\
35 "bcs_sourmash_matrix" \\
36 "The following table is an asymmetrical matrix of all <code>v.</code> all <b>ANI</b> values between each of the sample <b>FASTQ</b>'s sketch and genome <b>FASTA</b>'s sketch. Please note that there may be multiple genomes belonging to a serotype as processed by the initial screening steps of the workflow."
37 fi
38
39 cat <<-END_VERSIONS > versions.yml
40 "${task.process}":
41 python: \$( python --version | sed 's/Python //g' )
42 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
43 END_VERSIONS
44 """
45 }