Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/bcs_distance_matrix/main.nf @ 1:365849f031fd
"planemo upload"
| author | kkonganti |
|---|---|
| date | Mon, 05 Jun 2023 18:48:51 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 process BCS_DISTANCE_MATRIX { |
| kkonganti@1 | 2 tag "Samples vs Genomes" |
| kkonganti@1 | 3 label "process_pico" |
| kkonganti@1 | 4 |
| kkonganti@1 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}python${params.fs}3.8.1" : null) |
| kkonganti@1 | 6 conda (params.enable_conda ? "conda-forge::python=3.10 conda-forge::pyyaml" : null) |
| kkonganti@1 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@1 | 8 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : |
| kkonganti@1 | 9 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 input: |
| kkonganti@1 | 12 path matrix |
| kkonganti@1 | 13 path labels |
| kkonganti@1 | 14 |
| kkonganti@1 | 15 output: |
| kkonganti@1 | 16 path 'bcs_sourmash_matrix.tblsum.txt', emit: mqc_txt, optional: true |
| kkonganti@1 | 17 path 'bcs_sourmash_matrix_mqc.json' , emit: mqc_json, optional: true |
| kkonganti@1 | 18 path 'bcs_sourmash_matrix_mqc.yml' , emit: mqc_yml, optional: true |
| kkonganti@1 | 19 path 'versions.yml' , emit: versions |
| kkonganti@1 | 20 |
| kkonganti@1 | 21 when: |
| kkonganti@1 | 22 task.ext.when == null || task.ext.when |
| kkonganti@1 | 23 |
| kkonganti@1 | 24 script: |
| kkonganti@1 | 25 def args = task.ext.args ?: '' |
| kkonganti@1 | 26 |
| kkonganti@1 | 27 """ |
| kkonganti@1 | 28 sourmash_sim_matrix.py \\ |
| kkonganti@1 | 29 -pickle ${params.tuspy_ps} \\ |
| kkonganti@1 | 30 -csv $matrix \\ |
| kkonganti@1 | 31 -labels $labels |
| kkonganti@1 | 32 |
| kkonganti@1 | 33 if [ -e "bcs_sourmash_matrix.tblsum.txt" ] && [ -s "bcs_sourmash_matrix.tblsum.txt" ]; then |
| kkonganti@1 | 34 create_mqc_data_table.py \\ |
| kkonganti@1 | 35 "bcs_sourmash_matrix" \\ |
| kkonganti@1 | 36 "The following table is an asymmetrical matrix of all <code>v.</code> all <b>ANI</b> values between each of the sample <b>FASTQ</b>'s sketch and genome <b>FASTA</b>'s sketch. Please note that there may be multiple genomes belonging to a serotype as processed by the initial screening steps of the workflow." |
| kkonganti@1 | 37 fi |
| kkonganti@1 | 38 |
| kkonganti@1 | 39 cat <<-END_VERSIONS > versions.yml |
| kkonganti@1 | 40 "${task.process}": |
| kkonganti@1 | 41 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@1 | 42 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) |
| kkonganti@1 | 43 END_VERSIONS |
| kkonganti@1 | 44 """ |
| kkonganti@1 | 45 } |