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https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
Make all these tests pass
This commit is contained in:
FriederikeHanssen
parent
25a2a16f2d
commit
5e365d5eff
4 changed files with 97 additions and 95 deletions
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@ -34,7 +34,7 @@ process SEQKIT_SPLIT2 {
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fq.gz"), emit: reads
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tuple val(meta), path("*.split/*.fastq.gz"), emit: reads
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path("*.version.txt") , emit: version
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@ -44,7 +44,7 @@ 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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@ -54,15 +54,15 @@ process SEQKIT_SPLIT2 {
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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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// 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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@ -42,7 +42,7 @@ input:
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- reads:
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type: file
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description: FastQ files
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pattern: "*.{fq.gz/fastq.gz}"
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pattern: "*.fastq.gz"
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## TODO nf-core: Add a description of all of the variables used as output
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output:
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- meta:
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@ -53,7 +53,7 @@ output:
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- reads:
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type: file
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description: Split fastq files
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pattern: "*.{fq.gz}"
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pattern: "*.fastq.gz"
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- version:
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type: file
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description: File containing software version
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@ -2,54 +2,54 @@
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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 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
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include { SEQKIT_SPLIT2 as 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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// 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("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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// SEQKIT_SPLIT2_SIZE ( input )
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// }
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workflow test_seqkit_split2_part_single_end {
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workflow test_seqkit_split2_single_end_length {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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workflow test_seqkit_split2_single_end_size {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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workflow test_seqkit_split2_single_end_part {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_PART ( input )
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}
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// workflow test_seqkit_split2_length_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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workflow test_seqkit_split2_paired_end_length {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ]
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// SEQKIT_SPLIT2_LENGTH ( input )
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// }
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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// workflow test_seqkit_split2_size_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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workflow test_seqkit_split2_paired_end_size {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ]
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// SEQKIT_SPLIT2_SIZE ( input )
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// }
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SEQKIT_SPLIT2_SIZE ( input )
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}
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// workflow test_seqkit_split2_part_paired_end {
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// def input = []
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// input = [ [ id:'test', single_end:false ], // meta map
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// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ]
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workflow test_seqkit_split2_paired_end_part {
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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/fastq/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 +1,25 @@
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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 length
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_length -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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# - 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_split2_single_end_size -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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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -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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@ -26,30 +28,30 @@
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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_paired_end_length -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_paired_end_size -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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- name: seqkit split2 paired-end part
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command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -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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