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FastQC: actually run a test

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This commit is contained in:
Phil Ewels 2019-12-05 22:11:12 +01:00
parent ef486a908b
commit eb41e5ebba
7 changed files with 48 additions and 24 deletions
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14
nf-core/module_testing/check_process_outputs.nf Normal file
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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.preview.dsl = 2
cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
process check_output {
input:
val x from cheers
script:
"""
echo '$x world!'
"""
}

8
tools/fastqc/main.nf
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@ -1,15 +1,15 @@
process fastqc {
tag "$sample_id"
tag "FastQC - $sample_id"
publishDir "${params.outdir}/fastqc", mode: 'copy',
saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"}
container: 'quay.io/biocontainers/fastqc:0.11.8--2'
container 'quay.io/biocontainers/fastqc:0.11.8--2'
input:
set val(sample_id), file(reads)
tuple sample_id, path(reads)
output:
file "*_fastqc.{zip,html}"
path "*_fastqc.{zip,html}"
script:
"""

26
tools/fastqc/test/main.nf
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@ -1,13 +1,21 @@
#!/usr/bin/env nextflow
echo true
nextflow.preview.dsl = 2
include '../../../nf-core/module_testing/check_process_outputs.nf' params(params)
include '../main.nf' params(params)
cheers = Channel.from 'Bonjour', 'Ciao', 'Hello', 'Hola'
// Define input channels
readPaths = [
['SRR389222_sub1', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz']],
['SRR389222_sub2', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']],
['SRR389222_sub3', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub3.fastq.gz']]
]
Channel
.from(readPaths)
.map { row -> [ row[0], [row[1][0]]] }
.set { ch_read_files }
process sayHello {
input:
val x from cheers
script:
"""
echo '$x world!'
"""
// Run the workflow
workflow {
fastqc(ch_read_files)
// .check_output()
}

2
tools/fastqc/test/nextflow.config Normal file
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docker.enabled = true
params.outdir = './results'

6
tools/samtools/index/main.nf
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@ -1,13 +1,13 @@
process samtools_index {
tag "${bam.baseName}"
container: 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
input:
set file(bam)
path(bam)
output:
file "*.sorted.bam"
path "*.sorted.bam"
script:
def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'

6
tools/samtools/sort/main.nf
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@ -1,13 +1,13 @@
process samtools_index {
tag "${bam.baseName}"
container: 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
input:
set file(bam)
path(bam)
output:
file "*.bam.bai"
path "*.bam.bai"
script:
"""

10
tools/trim_galore/main.nf
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@ -7,15 +7,15 @@ process fastqc {
else filename
}
container: 'quay.io/biocontainers/trim-galore:0.6.5--0'
container 'quay.io/biocontainers/trim-galore:0.6.5--0'
input:
set val(sample_id), file(reads)
tuple sample_id, path(reads)
output:
set val(name), file("*fq.gz")
file "*trimming_report.txt"
file "*_fastqc.{zip,html}"
tuple name, path("*fq.gz")
path "*trimming_report.txt"
path "*_fastqc.{zip,html}"
script:
c_r1 = clip_r1 > 0 ? "--clip_r1 ${clip_r1}" : ''