Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/flye/assemble/main.nf @ 130:04f6ac8ca13c
planemo upload
| author | kkonganti |
|---|---|
| date | Wed, 03 Jul 2024 15:16:39 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process FLYE_ASSEMBLE { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_medium' |
| kkonganti@105 | 4 // errorStrategy 'ignore' |
| kkonganti@105 | 5 |
| kkonganti@105 | 6 module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.8" : null) |
| kkonganti@105 | 7 conda (params.enable_conda ? "bioconda::flye=2.8.1" : null) |
| kkonganti@105 | 8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 9 'https://depot.galaxyproject.org/singularity/flye:2.8.1--py37h8270d21_1' : |
| kkonganti@105 | 10 'quay.io/biocontainers/flye:2.8.1--py37h8270d21_1' }" |
| kkonganti@105 | 11 |
| kkonganti@105 | 12 input: |
| kkonganti@105 | 13 tuple val(meta), path(reads) |
| kkonganti@105 | 14 |
| kkonganti@105 | 15 output: |
| kkonganti@105 | 16 path "${meta.id}${params.fs}*" |
| kkonganti@105 | 17 tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true |
| kkonganti@105 | 18 path "versions.yml" , emit: versions |
| kkonganti@105 | 19 |
| kkonganti@105 | 20 when: |
| kkonganti@105 | 21 task.ext.when == null || task.ext.when |
| kkonganti@105 | 22 |
| kkonganti@105 | 23 script: |
| kkonganti@105 | 24 def args = task.ext.args ?: '' |
| kkonganti@105 | 25 """ |
| kkonganti@105 | 26 reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' ) |
| kkonganti@105 | 27 flye \\ |
| kkonganti@105 | 28 \$(echo "$args" | sed -e "s/\$reads_platform//") \\ |
| kkonganti@105 | 29 -t $task.cpus \\ |
| kkonganti@105 | 30 --out-dir "${meta.id}" \\ |
| kkonganti@105 | 31 \$reads_platform \\ |
| kkonganti@105 | 32 $reads |
| kkonganti@105 | 33 |
| kkonganti@105 | 34 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 35 "${task.process}": |
| kkonganti@105 | 36 flye: \$( flye --version ) |
| kkonganti@105 | 37 END_VERSIONS |
| kkonganti@105 | 38 |
| kkonganti@105 | 39 grepver="" |
| kkonganti@105 | 40 |
| kkonganti@105 | 41 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@105 | 42 grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' ) |
| kkonganti@105 | 43 else |
| kkonganti@105 | 44 grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' ) |
| kkonganti@105 | 45 fi |
| kkonganti@105 | 46 |
| kkonganti@105 | 47 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@105 | 48 grep: \$grepver |
| kkonganti@105 | 49 END_VERSIONS |
| kkonganti@105 | 50 """ |
| kkonganti@105 | 51 } |