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Make all these tests pass

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This commit is contained in:
FriederikeHanssen 2021-02-23 14:09:46 +01:00
parent 25a2a16f2d
commit 5e365d5eff
4 changed files with 97 additions and 95 deletions
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26
software/seqkit/split2/main.nf
View file

@ -34,7 +34,7 @@ process SEQKIT_SPLIT2 {
tuple val(meta), path(reads) tuple val(meta), path(reads)
output: output:
tuple val(meta), path("*.fq.gz"), emit: reads tuple val(meta), path("*.split/*.fastq.gz"), emit: reads
path("*.version.txt") , emit: version path("*.version.txt") , emit: version
@ -44,7 +44,7 @@ process SEQKIT_SPLIT2 {
//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. //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.
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
// if(meta.single_end){ if(meta.single_end){
""" """
seqkit \ seqkit \
split2 \ split2 \
@ -54,15 +54,15 @@ process SEQKIT_SPLIT2 {
echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
""" """
//} else { } else {
// """ """
// seqkit \ seqkit \
// split2 \ split2 \
// $options.args \ $options.args \
// --threads $task.cpus \ --threads $task.cpus \
// -1 ${reads[0]} \ -1 ${reads[0]} \
// -2 ${reads[1]} -2 ${reads[1]}
// echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
// """ """
//} }
} }

4
software/seqkit/split2/meta.yml
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@ -42,7 +42,7 @@ input:
- reads: - reads:
type: file type: file
description: FastQ files description: FastQ files
pattern: "*.{fq.gz/fastq.gz}" pattern: "*.fastq.gz"
## TODO nf-core: Add a description of all of the variables used as output ## TODO nf-core: Add a description of all of the variables used as output
output: output:
- meta: - meta:
@ -53,7 +53,7 @@ output:
- reads: - reads:
type: file type: file
description: Split fastq files description: Split fastq files
pattern: "*.{fq.gz}" pattern: "*.fastq.gz"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version

76
tests/software/seqkit/split2/main.nf
View file

@ -2,54 +2,54 @@
nextflow.enable.dsl = 2 nextflow.enable.dsl = 2
//include { SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] ) include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-length 26K'] )
//include { SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000' ] ) include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-size 5000' ] )
include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2'] ) include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/SEQKIT/SPLIT2/main.nf' addParams( options: ['args': '--by-part 2'] )
// workflow test_seqkit_split2_length_single_end { workflow test_seqkit_split2_single_end_length {
// def input = []
// input = [ [ id:'test', single_end:true ], // meta map
// file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
// SEQKIT_SPLIT2_LENGTH ( input )
// }
// workflow test_seqkit_split2_size_single_end {
// def input = []
// input = [ [ id:'test', single_end:true ], // meta map
// file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
// SEQKIT_SPLIT2_SIZE ( input )
// }
workflow test_seqkit_split2_part_single_end {
def input = [] def input = []
input = [ [ id:'test', single_end:true ], // meta map input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ] file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2_LENGTH ( input )
}
workflow test_seqkit_split2_single_end_size {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2_SIZE ( input )
}
workflow test_seqkit_split2_single_end_part {
def input = []
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/fastq/dna/SRR396636_R1.fastq.gz", checkIfExists: true) ]
SEQKIT_SPLIT2_PART ( input ) SEQKIT_SPLIT2_PART ( input )
} }
// workflow test_seqkit_split2_length_paired_end { workflow test_seqkit_split2_paired_end_length {
// def input = [] def input = []
// input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ] file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ]
// SEQKIT_SPLIT2_LENGTH ( input ) SEQKIT_SPLIT2_LENGTH ( input )
// } }
// workflow test_seqkit_split2_size_paired_end { workflow test_seqkit_split2_paired_end_size {
// def input = [] def input = []
// input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ] file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ]
// SEQKIT_SPLIT2_SIZE ( input ) SEQKIT_SPLIT2_SIZE ( input )
// } }
// workflow test_seqkit_split2_part_paired_end { workflow test_seqkit_split2_paired_end_part {
// def input = [] def input = []
// input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
// file("${launchDir}/tests/data/dna/SRR396636_*", checkIfExists: true) ] file("${launchDir}/tests/data/fastq/dna/SRR396636_*", checkIfExists: true) ]
// SEQKIT_SPLIT2_PART ( input ) SEQKIT_SPLIT2_PART ( input )
// } }

86
tests/software/seqkit/split2/test.yml
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@ -1,23 +1,25 @@
# - name: seqkit split2 single-end length - name: seqkit split2 single-end length
# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_length -c tests/config/nextflow.config
# tags: tags:
# - seqkit - seqkit
# - seqkit_split2 - seqkit_split2
# - seqkit_split2_single_end - seqkit_split2_single_end
# - length - length
files:
- path: output/seqkit/
# - name: seqkit split2 single-end size - name: seqkit split2 single-end size
# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_stest_seqkit_split2_size_single_endplit2_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_size -c tests/config/nextflow.config
# tags: tags:
# - seqkit - seqkit
# - seqkit_split2 - seqkit_split2
# - seqkit_split2_single_end - seqkit_split2_single_end
# - size - size
# files: files:
# - path: output/seqkit/ - path: output/seqkit/
- name: seqkit split2 single-end part - name: seqkit split2 single-end part
command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_part_single_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_single_end_part -c tests/config/nextflow.config
tags: tags:
- seqkit - seqkit
- seqkit_split2 - seqkit_split2
@ -26,30 +28,30 @@
files: files:
- path: output/seqkit/ - path: output/seqkit/
# - name: seqkit split2 paired-end length - name: seqkit split2 paired-end length
# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_length_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_length -c tests/config/nextflow.config
# tags: tags:
# - seqkit - seqkit
# - seqkit_split2 - seqkit_split2
# - seqkit_split2_paired_end - seqkit_split2_paired_end
# - length - length
# files: files:
# - path: output/seqkit/ - path: output/seqkit/
# - name: seqkit split2 paired-end size - name: seqkit split2 paired-end size
# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_size_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_size -c tests/config/nextflow.config
# tags: tags:
# - seqkit - seqkit
# - seqkit_split2 - seqkit_split2
# - seqkit_split2_paired_end - seqkit_split2_paired_end
# - size - size
# files: files:
# - path: output/seqkit/ - path: output/seqkit/
# - name: seqkit split2 paired-end part - name: seqkit split2 paired-end part
# command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_part_paired_end -c tests/config/nextflow.config command: nextflow run ./tests/software/seqkit/split2 -entry test_seqkit_split2_paired_end_part -c tests/config/nextflow.config
# tags: tags:
# - seqkit - seqkit
# - seqkit_split2 - seqkit_split2
# - seqkit_split2_paired_end - seqkit_split2_paired_end
# - part - part