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https://github.com/MillironX/nf-core_modules.git
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Try to make a single test pass
This commit is contained in:
FriederikeHanssen
parent
a0c9777d60
commit
25a2a16f2d
4 changed files with 88 additions and 112 deletions
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@ -1,12 +1,6 @@
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
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// https://github.com/nf-core/modules/tree/master/software
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// You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
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// https://nf-co.re/join
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// TODO nf-core: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
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// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
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// All other parameters MUST be provided as a string i.e. "options.args"
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// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
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@ -39,16 +33,9 @@ process SEQKIT_SPLIT2 {
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input:
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tuple val(meta), path(reads)
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// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
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// MUST be provided as an input via a Groovy Map called "meta".
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// This information may not be required in some instances e.g. indexing reference genome files:
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// https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
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// TODO nf-core: Where applicable please provide/convert compressed files as input/output
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// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
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output:
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tuple val(meta), path("*.fq.gz"), emit: reads
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path("*.version.txt") , emit: version
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path("*.version.txt") , emit: version
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script:
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@ -57,29 +44,25 @@ process SEQKIT_SPLIT2 {
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//TODO not sure if this is useful here, as the splits need to be named individually, and this would make the prefix the same and the outputname I am afraid.
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if(meta.single_end){
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// if(meta.single_end){
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 $reads \
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-O $prefix
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-1 $reads
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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} else {
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"""
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seqkit \
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split2 \
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$options.args \
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--threads $task.cpus \
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-1 ${reads[0]} \
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-2 ${reads[1]} \
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-O $prefix
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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//} else {
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// """
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// seqkit \
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// split2 \
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// $options.args \
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// --threads $task.cpus \
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// -1 ${reads[0]} \
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// -2 ${reads[1]}
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// echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
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// """
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//}
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}
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@ -1,12 +1,10 @@
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name: seqkit_split2
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## TODO nf-core: Add a description and keywords
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description: Split single or paired-end fastq.gz files
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keywords:
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- split
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- fastq
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tools:
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- seqkit:
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## TODO nf-core: Add a description and other details for the software below
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description: |
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Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
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homepage: https://github.com/shenwei356/seqkit
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@ -2,25 +2,25 @@
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nextflow.enable.dsl = 2
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include { SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
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include { SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000 ' ] )
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include { SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2 '] )
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//include { SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
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//include { SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2'] )
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workflow test_seqkit_split2_length_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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// workflow test_seqkit_split2_length_single_end {
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// def input = []
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// input = [ [ id:'test', single_end:true ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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// SEQKIT_SPLIT2_LENGTH ( input )
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// }
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workflow test_seqkit_split2_size_single_end {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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// workflow test_seqkit_split2_size_single_end {
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// def input = []
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// input = [ [ id:'test', single_end:true ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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// SEQKIT_SPLIT2_SIZE ( input )
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// }
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workflow test_seqkit_split2_part_single_end {
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def input = []
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@ -30,26 +30,26 @@ workflow test_seqkit_split2_part_single_end {
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SEQKIT_SPLIT2_PART ( input )
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}
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workflow test_seqkit_split2_length_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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// workflow test_seqkit_split2_length_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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// SEQKIT_SPLIT2_LENGTH ( input )
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// }
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workflow test_seqkit_split2_size_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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// workflow test_seqkit_split2_size_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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// SEQKIT_SPLIT2_SIZE ( input )
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// }
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workflow test_seqkit_split2_part_paired_end {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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// workflow test_seqkit_split2_part_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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SEQKIT_SPLIT2_PART ( input )
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}
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// SEQKIT_SPLIT2_PART ( input )
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// }
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@ -1,23 +1,20 @@
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- name: seqkit split2 single-end length
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_single_end -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit_split2
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- seqkit_split2_single_end
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- length
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files:
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- path: output/seqkit/
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md5sum: a41bfadacd2eeef1d31e05c135cc4f4e
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# - name: seqkit split2 single-end length
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# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_single_end -c tests/config/nextflow.config
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# tags:
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# - seqkit
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# - seqkit_split2
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# - seqkit_split2_single_end
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# - length
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- name: seqkit split2 single-end size
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_stest_seqkit_split2_size_single_endplit2_single_end -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit_split2
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- seqkit_split2_single_end
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- size
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files:
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- path: output/seqkit/
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# - name: seqkit split2 single-end size
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# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_stest_seqkit_split2_size_single_endplit2_single_end -c tests/config/nextflow.config
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# tags:
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# - seqkit
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# - seqkit_split2
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# - seqkit_split2_single_end
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# - size
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# files:
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# - path: output/seqkit/
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- name: seqkit split2 single-end part
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_part_single_end -c tests/config/nextflow.config
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files:
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- path: output/seqkit/
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- name: seqkit split2 paired-end length
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_paired_end -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit_split2
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- seqkit_split2_paired_end
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- length
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files:
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- path: output/seqkit/
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# - name: seqkit split2 paired-end length
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# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_paired_end -c tests/config/nextflow.config
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# tags:
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# - seqkit
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# - seqkit_split2
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# - seqkit_split2_paired_end
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# - length
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# files:
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# - path: output/seqkit/
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- name: seqkit split2 paired-end size
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_size_paired_end -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit_split2
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- seqkit_split2_paired_end
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- size
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files:
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- path: output/seqkit/
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# - name: seqkit split2 paired-end size
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# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_size_paired_end -c tests/config/nextflow.config
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# tags:
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# - seqkit
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# - seqkit_split2
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# - seqkit_split2_paired_end
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# - size
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# files:
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# - path: output/seqkit/
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- name: seqkit split2 paired-end part
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_part_paired_end -c tests/config/nextflow.config
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tags:
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- seqkit
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- seqkit_split2
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- seqkit_split2_paired_end
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- part
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files:
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- path: output/seqkit/
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# - name: seqkit split2 paired-end part
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# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_part_paired_end -c tests/config/nextflow.config
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# tags:
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# - seqkit
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# - seqkit_split2
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# - seqkit_split2_paired_end
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# - part
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