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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-04-10 07:30:45 +02:00 committed by GitHub
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72 changed files with 1451 additions and 122 deletions
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42
modules/adapterremoval/main.nf
View file

@ -12,14 +12,13 @@ process ADAPTERREMOVAL {
path(adapterlist)
output:
tuple val(meta), path("${prefix}.truncated.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair1.truncated.gz") , optional: true, emit: pair1_truncated
tuple val(meta), path("${prefix}.pair2.truncated.gz") , optional: true, emit: pair2_truncated
tuple val(meta), path("${prefix}.collapsed.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.truncated.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.paired.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path('*.log') , emit: log
tuple val(meta), path("${prefix}.truncated.fastq.gz") , optional: true, emit: singles_truncated
tuple val(meta), path("${prefix}.discarded.fastq.gz") , optional: true, emit: discarded
tuple val(meta), path("${prefix}.pair{1,2}.truncated.fastq.gz") , optional: true, emit: paired_truncated
tuple val(meta), path("${prefix}.collapsed.fastq.gz") , optional: true, emit: collapsed
tuple val(meta), path("${prefix}.collapsed.truncated.fastq.gz") , optional: true, emit: collapsed_truncated
tuple val(meta), path("${prefix}.paired.fastq.gz") , optional: true, emit: paired_interleaved
tuple val(meta), path('*.settings') , emit: settings
path "versions.yml" , emit: versions
when:
@ -38,10 +37,19 @@ process ADAPTERREMOVAL {
$adapterlist \\
--basename ${prefix} \\
--threads ${task.cpus} \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
@ -56,10 +64,24 @@ process ADAPTERREMOVAL {
$adapterlist \\
--basename ${prefix} \\
--threads $task.cpus \\
--settings ${prefix}.log \\
--seed 42 \\
--gzip
ensure_fastq() {
if [ -f "\${1}" ]; then
mv "\${1}" "\${1::-3}.fastq.gz"
fi
}
ensure_fastq '${prefix}.truncated.gz'
ensure_fastq '${prefix}.discarded.gz'
ensure_fastq '${prefix}.pair1.truncated.gz'
ensure_fastq '${prefix}.pair2.truncated.gz'
ensure_fastq '${prefix}.collapsed.gz'
ensure_fastq '${prefix}.collapsed.truncated.gz'
ensure_fastq '${prefix}.paired.gz'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
adapterremoval: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")

14
modules/adapterremoval/meta.yml
View file

@ -43,43 +43,43 @@ output:
Adapter trimmed FastQ files of either single-end reads, or singleton
'orphaned' reads from merging of paired-end data (i.e., one of the pair
was lost due to filtering thresholds).
pattern: "*.truncated.gz"
pattern: "*.truncated.fastq.gz"
- discarded:
type: file
description: |
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
pattern: "*.discarded.gz"
pattern: "*.discarded.fastq.gz"
- pair1_truncated:
type: file
description: |
Adapter trimmed R1 FastQ files of paired-end reads that did not merge
with their respective R2 pair due to long templates. The respective pair
is stored in 'pair2_truncated'.
pattern: "*.pair1.truncated.gz"
pattern: "*.pair1.truncated.fastq.gz"
- pair2_truncated:
type: file
description: |
Adapter trimmed R2 FastQ files of paired-end reads that did not merge
with their respective R1 pair due to long templates. The respective pair
is stored in 'pair1_truncated'.
pattern: "*.pair2.truncated.gz"
pattern: "*.pair2.truncated.fastq.gz"
- collapsed:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
pattern: "*.collapsed.gz"
pattern: "*.collapsed.fastq.gz"
- collapsed_truncated:
type: file
description: |
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair and were trimmed of adapter due to sufficient overlap.
pattern: "*.collapsed.truncated.gz"
pattern: "*.collapsed.truncated.fastq.gz"
- log:
type: file
description: AdapterRemoval log file
pattern: "*.log"
pattern: "*.settings"
- versions:
type: file
description: File containing software versions

6
modules/biobambam/bammarkduplicates2/main.nf
View file

@ -2,10 +2,8 @@ process BIOBAMBAM_BAMMARKDUPLICATES2 {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::biobambam=2.0.182" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/biobambam:2.0.182--h7d875b9_0':
'quay.io/biocontainers/biobambam:2.0.182--h7d875b9_0' }"
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
input:
tuple val(meta), path(bam)

46
modules/biobambam/bamsormadup/main.nf Normal file
View file

@ -0,0 +1,46 @@
process BIOBAMBAM_BAMSORMADUP {
tag "$meta.id"
label "process_medium"
conda (params.enable_conda ? "bioconda::biobambam=2.0.183" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/biobambam:2.0.183--h9f5acd7_1' : 'quay.io/biocontainers/biobambam:2.0.183--h9f5acd7_1'}"
input:
tuple val(meta), path(bams)
path(fasta)
output:
tuple val(meta), path("*.{bam,cram}") ,emit: bam
tuple val(meta), path("*.bam.bai") ,optional:true, emit: bam_index
tuple val(meta), path("*.metrics.txt") ,emit: metrics
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def suffix = args.contains("outputformat=cram") ? "cram" : "bam"
def input_string = bams.join(" I=")
if (args.contains("outputformat=cram") && reference == null) error "Reference required for CRAM output."
"""
bamcat \\
I=${input_string} \\
level=0 \\
| bamsormadup \\
$args \\
M=${prefix}.metrics.txt \\
tmpfile=$prefix \\
threads=$task.cpus \\
> ${prefix}.${suffix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bamcat: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
bamsormadup: \$(echo \$(bamsormadup --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' )
END_VERSIONS
"""
}

52
modules/biobambam/bamsormadup/meta.yml Normal file
View file

@ -0,0 +1,52 @@
name: biobambam_bamsormadup
description: Parallel sorting and duplicate marking
keywords:
- markduplicates
- sort
- bam
- cram
tools:
- biobambam:
description: |
biobambam is a set of tools for early stage alignment file processing.
homepage: https://gitlab.com/german.tischler/biobambam2
documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
doi: 10.1186/1751-0473-9-13
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bams:
type: file
description: List containing 1 or more bam files
- fasta:
type: file
description: Reference genome in FASTA format (optional)
pattern: "*.{fa,fasta}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM file with duplicate reads marked/removed
pattern: "*.{bam,cram}"
- bam_index:
type: file
description: BAM index file
pattern: "*.{bai}"
- metrics:
type: file
description: Duplicate metrics file generated by biobambam
pattern: "*.{metrics.txt}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@matthdsm"

10
modules/centrifuge/main.nf → modules/centrifuge/centrifuge/main.nf
View file

@ -1,4 +1,4 @@
process CENTRIFUGE {
process CENTRIFUGE_CENTRIFUGE {
tag "$meta.id"
label 'process_high'
@ -17,7 +17,6 @@ process CENTRIFUGE {
output:
tuple val(meta), path('*report.txt') , emit: report
tuple val(meta), path('*results.txt') , emit: results
tuple val(meta), path('*kreport.txt') , emit: kreport
tuple val(meta), path('*.sam') , optional: true, emit: sam
tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
@ -30,7 +29,6 @@ process CENTRIFUGE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
def db_name = db.toString().replace(".tar.gz","")
def unaligned = ''
def aligned = ''
if (meta.single_end) {
@ -42,9 +40,10 @@ process CENTRIFUGE {
}
def sam_output = sam_format ? "--out-fmt 'sam'" : ''
"""
tar -xf $db
## we add "-no-name ._" to ensure silly Mac OSX metafiles files aren't included
db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
centrifuge \\
-x $db_name \\
-x \$db_name \\
-p $task.cpus \\
$paired \\
--report-file ${prefix}.report.txt \\
@ -53,7 +52,6 @@ process CENTRIFUGE {
$aligned \\
$sam_output \\
$args
centrifuge-kreport -x $db_name ${prefix}.results.txt > ${prefix}.kreport.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":

11
modules/centrifuge/meta.yml → modules/centrifuge/centrifuge/meta.yml
View file

@ -1,4 +1,4 @@
name: centrifuge
name: centrifuge_centrifuge
description: Classifies metagenomic sequence data
keywords:
- classify
@ -25,8 +25,7 @@ input:
respectively.
- db:
type: directory
description: Centrifuge database in .tar.gz format
pattern: "*.tar.gz"
description: Path to directory containing centrifuge database files
- save_unaligned:
type: value
description: If true unmapped fastq files are saved
@ -49,12 +48,6 @@ output:
description: |
File containing classification results
pattern: "*.{results.txt}"
- kreport:
type: file
description: |
File containing kraken-style report from centrifuge
out files.
pattern: "*.{kreport.txt}"
- fastq_unmapped:
type: file
description: Unmapped fastq files

2
modules/cnvpytor/histogram/main.nf
View file

@ -32,7 +32,7 @@ process CNVPYTOR_HISTOGRAM {
stub:
"""
touch test.pytor
touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":

2
modules/cnvpytor/partition/main.nf
View file

@ -32,7 +32,7 @@ process CNVPYTOR_PARTITION {
stub:
"""
touch test.pytor
touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":

13
modules/controlfreec/assesssignificance/main.nf
View file

@ -21,7 +21,7 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
cat \$(which assess_significance.R) | R --slave --args ${cnvs} ${ratio}
mv *.p.value.txt ${prefix}.p.value.txt
@ -30,4 +30,15 @@ process CONTROLFREEC_ASSESSSIGNIFICANCE {
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.p.value.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

20
modules/controlfreec/freec/main.nf
View file

@ -21,7 +21,7 @@ process CONTROLFREEC_FREEC {
output:
tuple val(meta), path("*_ratio.BedGraph") , emit: bedgraph, optional: true
tuple val(meta), path("*_control.cpn") , emit: control_cpn
tuple val(meta), path("*_control.cpn") , emit: control_cpn, optional: true
tuple val(meta), path("*_sample.cpn") , emit: sample_cpn
tuple val(meta), path("GC_profile.*.cpn") , emit: gcprofile_cpn, optional:true
tuple val(meta), path("*_BAF.txt") , emit: BAF
@ -155,4 +155,22 @@ process CONTROLFREEC_FREEC {
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_ratio.BedGraph
touch ${prefix}_sample.cpn
touch GC_profile.${prefix}.cpn
touch ${prefix}_BAF.txt
touch ${prefix}_CNVs
touch ${prefix}_info.txt
touch ${prefix}_ratio.txt
touch config.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

11
modules/controlfreec/freec2bed/main.nf
View file

@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2BED {
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

11
modules/controlfreec/freec2circos/main.nf
View file

@ -28,4 +28,15 @@ process CONTROLFREEC_FREEC2CIRCOS {
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.circos.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

14
modules/controlfreec/makegraph/main.nf
View file

@ -25,12 +25,24 @@ process CONTROLFREEC_MAKEGRAPH {
def prefix = task.ext.prefix ?: "${meta.id}"
def baf = baf ?: ""
"""
cat /usr/local/bin/makeGraph.R | R --slave --args ${args} ${ratio} ${baf}
cat \$(which makeGraph.R) | R --slave --args ${args} ${ratio} ${baf}
mv *_BAF.txt.png ${prefix}_BAF.png
mv *_ratio.txt.log2.png ${prefix}_ratio.log2.png
mv *_ratio.txt.png ${prefix}_ratio.png
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}_BAF.png
touch ${prefix}_ratio.log2.png
touch ${prefix}_ratio.png
cat <<-END_VERSIONS > versions.yml
"${task.process}":

4
modules/dastool/dastool/main.nf
View file

@ -14,8 +14,8 @@ process DASTOOL_DASTOOL {
output:
tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("*_summary.tsv") , emit: summary
tuple val(meta), path("*_DASTool_contig2bin.tsv") , emit: contig2bin
tuple val(meta), path("*_summary.tsv") , optional: true, emit: summary
tuple val(meta), path("*_DASTool_contig2bin.tsv") , optional: true, emit: contig2bin
tuple val(meta), path("*.eval") , optional: true, emit: eval
tuple val(meta), path("*_DASTool_bins/*.fa") , optional: true, emit: bins
tuple val(meta), path("*.pdf") , optional: true, emit: pdfs

6
modules/dshbio/exportsegments/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_EXPORTSEGMENTS {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(gfa)

6
modules/dshbio/filterbed/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_FILTERBED {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

6
modules/dshbio/filtergff3/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_FILTERGFF3 {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(gff3)

6
modules/dshbio/splitbed/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_SPLITBED {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

6
modules/dshbio/splitgff3/main.nf
View file

@ -2,10 +2,10 @@ process DSHBIO_SPLITGFF3 {
tag "${meta.id}"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.7" : null)
conda (params.enable_conda ? "bioconda::dsh-bio=2.0.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.7--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.7--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dsh-bio:2.0.8--hdfd78af_0' :
'quay.io/biocontainers/dsh-bio:2.0.8--hdfd78af_0' }"
input:
tuple val(meta), path(gff3)

51
modules/picard/crosscheckfingerprints/main.nf Normal file
View file

@ -0,0 +1,51 @@
process PICARD_CROSSCHECKFINGERPRINTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input:
tuple val(meta), path(input1)
path input2
path haplotype_map
output:
tuple val(meta), path("*.crosscheck_metrics.txt"), emit: crosscheck_metrics
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def input1_string = input1.join(" --INPUT ")
def input2_string = input2 ? "--SECOND_INPUT " + input2.join(" --SECOND_INPUT ") : ""
def avail_mem = 3
if (!task.memory) {
log.info '[Picard CrosscheckFingerprints] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
CrosscheckFingerprints \\
$args \\
--NUM_THREADS ${task.cpus} \\
--INPUT $input1_string \\
$input2_string \\
--HAPLOTYPE_MAP ${haplotype_map} \\
--OUTPUT ${prefix}.crosscheck_metrics.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$( picard CrosscheckFingerprints --version 2>&1 | grep -o 'Version:.*' | cut -f2- -d: )
END_VERSIONS
"""
}

53
modules/picard/crosscheckfingerprints/meta.yml Normal file
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@ -0,0 +1,53 @@
name: "picard_crosscheckfingerprints"
description: Checks that all data in the set of input files appear to come from the same individual
keywords:
- alignment
- metrics
- statistics
- fingerprint
- bam
tools:
- picard:
description: |
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS)
data and formats such as SAM/BAM/CRAM and VCF.
homepage: https://broadinstitute.github.io/picard/
documentation: https://broadinstitute.github.io/picard/
tool_dev_url: https://github.com/broadinstitute/picard/
licence: ["MIT"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input1:
type: file
description: List containing 1 or more bam/vcf files or a file containing filepaths
pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
- input2:
type: file
description: Optional list containing 1 or more bam/vcf files or a file containing filepaths
pattern: "*.{bam,vcf,vcf.gz,txt,fofn}"
- haplotype_map:
type: file
description: Haplotype map file
pattern: "*.{txt,vcf,vcf.gz}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- crosscheck_metrics:
type: file
description: Metrics created by crosscheckfingerprints
pattern: "*.{crosscheck_metrics.txt}"
authors:
- "@matthdsm"

49
modules/picard/liftovervcf/main.nf Normal file
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@ -0,0 +1,49 @@
process PICARD_LIFTOVERVCF {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::picard=2.26.10" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/picard:2.26.10--hdfd78af_0' :
'quay.io/biocontainers/picard:2.26.10--hdfd78af_0' }"
input:
tuple val(meta), path(input_vcf)
path dict
path chain
path fasta
output:
tuple val(meta), path("*lifted.vcf.gz") , emit: vcf_lifted
tuple val(meta), path("*unlifted.vcf.gz"), emit: vcf_unlifted
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def avail_mem = 1
if (!task.memory) {
log.info '[Picard LiftoverVcf] Available memory not known - defaulting to 1GB. Specify process memory requirements to change this.'
} else {
avail_mem = task.memory.giga
}
"""
picard \\
-Xmx${avail_mem}g \\
LiftoverVcf \\
$args \\
I=$input_vcf \\
O=${prefix}.lifted.vcf.gz \\
CHAIN=$chain \\
REJECT=${prefix}.unlifted.vcf.gz \\
R=$fasta
cat <<-END_VERSIONS > versions.yml
"${task.process}":
picard: \$(picard LiftoverVcf --version 2>&1 | grep -o 'Version.*' | cut -f2- -d:)
END_VERSIONS
"""
}

55
modules/picard/liftovervcf/meta.yml Normal file
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@ -0,0 +1,55 @@
name: picard_liftovervcf
description: convert between genome builds
keywords:
- liftOver
- picard
tools:
- picard:
description: Move annotations from one assembly to another
homepage: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard
tool_dev_url: https://github.com/broadinstitute/picard
doi: ""
licence: ["MIT"]
input:
- meta:
type: map
description: Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- input_vcf:
type: file
description: VCF file
pattern: "*.{vcf,vcf.gz}"
- chain:
type: file
description: The liftover chain file
- fasta:
type: file
description: fasta file
pattern: "*.fasta"
- dict:
type: file
description: dictionary for fasta file
pattern: "*.{dict}"
output:
- meta:
type: map
description: Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- vcf_lifted:
type: file
description: VCF file containing successfully lifted variants
pattern: "*.{lifted.vcf.gz}"
- vcf_unlifted:
type: file
description: VCF file containing unsuccessfully lifted variants
pattern: "*.{unlifted.vcf.gz}"
authors:
- "@lucpen"

61
modules/prinseqplusplus/main.nf Normal file
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@ -0,0 +1,61 @@
process PRINSEQPLUSPLUS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::prinseq-plus-plus=1.2.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/prinseq-plus-plus:1.2.3--hc90279e_1':
'quay.io/biocontainers/prinseq-plus-plus:1.2.3--hc90279e_1' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*_good_out*.fastq.gz") , emit: good_reads
tuple val(meta), path("*_single_out*.fastq.gz"), optional: true, emit: single_reads
tuple val(meta), path("*_bad_out*.fastq.gz") , optional: true, emit: bad_reads
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (meta.single_end) {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
} else {
"""
prinseq++ \\
-threads $task.cpus \\
-fastq ${reads[0]} \\
-fastq2 ${reads[1]} \\
-out_name ${prefix} \\
-out_gz \\
-VERBOSE 1 \\
$args \\
| tee ${prefix}.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
prinseqplusplus: \$(echo \$(prinseq++ --version | cut -f 2 -d ' ' ))
END_VERSIONS
"""
}
}

60
modules/prinseqplusplus/meta.yml Normal file
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@ -0,0 +1,60 @@
name: "prinseqplusplus"
description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data
keywords:
- fastq
- fasta
- filter
- trim
tools:
- "prinseqplusplus":
description: "PRINSEQ++ - Multi-threaded C++ sequence cleaning"
homepage: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
documentation: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus"
doi: "10.7287/peerj.preprints.27553v1"
licence: "['GPL v2']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: |
List of input FastQ files of size 1 and 2 for single-end and paired-end
data, respectively.
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- good_reads:
type: file
description: Reads passing filter(s) in gzipped FASTQ format
pattern: "*_good_out_{R1,R2}.fastq.gz"
- single_reads:
type: file
description: |
Single reads without the pair passing filter(s) in gzipped FASTQ format
pattern: "*_single_out_{R1,R2}.fastq.gz"
- bad_reads:
type: file
description: |
Reads without not passing filter(s) in gzipped FASTQ format
pattern: "*_bad_out_{R1,R2}.fastq.gz"
- log:
type: file
description: |
Verbose level 2 STDOUT information in a log file
pattern: "*.log"
authors:
- "@jfy133"

59
modules/snapaligner/index/main.nf Normal file
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@ -0,0 +1,59 @@
process SNAPALIGNER_INDEX {
tag '$fasta'
label 'process_high'
conda (params.enable_conda ? "bioconda::snap-aligner=2.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snap-aligner:2.0.1--hd03093a_1':
'quay.io/biocontainers/snap-aligner:2.0.1--hd03093a_1' }"
input:
path fasta
path altcontigfile
path nonaltcontigfile
path altliftoverfile
output:
path "snap/*" ,emit: index
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def altcontigfile_arg = altcontigfile ? '-altContigFile ' + altcontigfile : ''
def nonaltcontigfile_arg = nonaltcontigfile ? '-nonAltContigFile ' + nonaltcontigfile : ''
def altliftoverfile_arg = altliftoverfile ? '-altLiftoverFile ' + altliftoverfile : ''
"""
mkdir snap
snap-aligner \\
index \\
$fasta \\
snap \\
-t${task.cpus} \\
$altcontigfile_arg \\
$nonaltcontigfile_arg \\
$altliftoverfile_arg \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //')
END_VERSIONS
"""
stub:
"""
mkdir snap
echo "Genome" > snap/Genome
echo "GenomeIndex" > snap/GenomeIndex
echo "GenomeIndexHash" > snap/GenomeIndexHash
echo "OverflowTable" > snap/OverflowTable
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snapaligner: \$(snap-aligner 2>&1| head -n 1 | sed 's/^.*version //;s/\.\$//')
END_VERSIONS
"""
}

39
modules/snapaligner/index/meta.yml Normal file
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@ -0,0 +1,39 @@
name: "snapaligner_index"
description: Create a SNAP index for reference genome
keywords:
- index
- fasta
- genome
- reference
tools:
- "snapaligner":
description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
homepage: "http://snap.cs.berkeley.edu"
documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
tool_dev_url: "https://github.com/amplab/snap"
doi: "10.1101/2021.11.23.469039"
licence: "['Apache v2']"
input:
- fasta:
type: file
description: Input genome fasta file
- altcontigfile:
type: file
description: Optional file with a list of alt contig names, one per line.
- nonaltcontigfile:
type: file
description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size.
- altliftoverfile:
type: file
description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit.
output:
- index:
type: file
description: SNAP genome index files
pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@matthdsm"

61
modules/stadeniolib/scramble/main.nf Normal file
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@ -0,0 +1,61 @@
process STADENIOLIB_SCRAMBLE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::staden_io_lib=1.14.14" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/staden_io_lib:1.14.14--h0d9da7e_3' :
'quay.io/biocontainers/staden_io_lib:1.14.14--h0d9da7e_3' }"
input:
tuple val(meta), path(reads)
path(fasta)
path(fai)
path(gzi)
output:
tuple val(meta), path("*.cram") ,emit: cram
path "*.gzi" ,emit: gzi, optional: true
path "versions.yml" ,emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def inputformat = reads.getExtension
def outputformat = "cram"
if ("-O sam" in args) {
outputformat = "sam"
} else if ("-O bam" in args) {
outputformat = "bam"
}
def reference = if fasta && fai : "--r ${fasta}" else ""
if (outputformat == "cram" && !reference) {
error "Cannot convert to CRAM without a reference"
}
def gz_index = if gzi : "--g ${gzi}" else ""
if (outputformat == "cram" || outputformat == "sam") {
gz_index = ""
warning "Cannot use gzip index for CRAM or SAM output"
}
"""
scramble \
$args \
-I ${inputformat} \
$reference \
-t $task.cpus \
${reads} \
${prefix}.${outputformat}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
stadeniolib: \$(echo \$(scramble -h | head -n 1 |sed 's/^.*version //'))
END_VERSIONS
"""
}

58
modules/stadeniolib/scramble/meta.yml Normal file
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@ -0,0 +1,58 @@
name: "stadeniolib_scramble"
description: Advanced sequence file format conversions
keywords:
- sam
- bam
- cram
- compression
tools:
- "scramble":
description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats."
homepage: "https://github.com/jkbonfield/io_lib"
documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
tool_dev_url: "https://github.com/jkbonfield/io_lib"
licence: "['BSD']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
- fasta:
type: file
description: Reference genome in FASTA format
pattern: "*.{fa,fasta}"
- fai:
type: file
description: FASTA index file from samtools faidx
pattern: "*.{fai}"
- gzi:
type: file
description: Optional gzip index file for BAM inputs
pattern: "*.gzi"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- reads:
type: file
description: Converted reads
pattern: "*.{sam, bam, cram}"
- gzi:
type: Optional file
description: gzip index file for BAM outputs
pattern: ".{bam.gzi}"
authors:
- "@matthdsm"

6
modules/untar/main.nf
View file

@ -2,10 +2,10 @@ process UNTAR {
tag "$archive"
label 'process_low'
conda (params.enable_conda ? "conda-forge::tar=1.32" : null)
conda (params.enable_conda ? "conda-forge::tar=1.34" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
'biocontainers/biocontainers:v1.2.0_cv1' }"
'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv2/biocontainers_v1.2.0_cv2.img' :
'biocontainers/biocontainers:v1.2.0_cv2' }"
input:
tuple val(meta), path(archive)

50
subworkflows/nf-core/homer/groseq/main.nf Normal file
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@ -0,0 +1,50 @@
/*
* Identify transcripts with homer
*/
include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main'
include { HOMER_MAKEUCSCFILE } from '../../../../modules/homer/makeucscfile/main'
include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main'
include { HOMER_POS2BED } from '../../../../modules/homer/pos2bed/main'
workflow HOMER_GROSEQ {
take:
bam // channel: [ val(meta), [ reads ] ]
fasta // file: /path/to/bwa/index/
main:
ch_versions = Channel.empty()
/*
* Create a Tag Directory From The GRO-Seq experiment
*/
HOMER_MAKETAGDIRECTORY ( bam, fasta )
ch_versions = ch_versions.mix(HOMER_MAKETAGDIRECTORY.out.versions.first())
/*
* Creating UCSC Visualization Files
*/
HOMER_MAKEUCSCFILE ( HOMER_MAKETAGDIRECTORY.out.tagdir )
ch_versions = ch_versions.mix(HOMER_MAKEUCSCFILE.out.versions.first())
/*
* Find transcripts directly from GRO-Seq
*/
HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
ch_versions = ch_versions.mix(HOMER_FINDPEAKS.out.versions.first())
/*
* Convert peak file to bed file
*/
HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
ch_versions = ch_versions.mix(HOMER_POS2BED.out.versions.first())
emit:
tagdir = HOMER_MAKETAGDIRECTORY.out.tagdir // channel: [ val(meta), [ tagdir ] ]
bed_graph = HOMER_MAKEUCSCFILE.out.bedGraph // channel: [ val(meta), [ tag_dir/*ucsc.bedGraph.gz ] ]
peaks = HOMER_FINDPEAKS.out.txt // channel: [ val(meta), [ *peaks.txt ] ]
bed = HOMER_POS2BED.out.bed // channel: [ val(meta), [ *peaks.txt ] ]
versions = ch_versions // channel: [ versions.yml ]
}

48
subworkflows/nf-core/homer/groseq/meta.yml Normal file
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@ -0,0 +1,48 @@
name: homer_groseq
description: Perform variant calling on a set of normal samples using mutect2 panel of normals mode. Group them into a genomicsdbworkspace using genomicsdbimport, then use this to create a panel of normals using createsomaticpanelofnormals.
keywords:
- homer
- groseq
- nascent
modules:
- homer/maketagdirectory
- homer/makeucscfile
- homer/findpeaks
- homer/pos2bed
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- input:
type: list
description: list of BAM files, also able to take SAM and BED as input
pattern: "[ *.{bam/sam/bed} ]"
- fasta:
type: file
description: The reference fasta file
pattern: "*.fasta"
output:
- tagdir:
type: directory
description: The "Tag Directory"
pattern: "*_tagdir"
- bedGraph:
type: file
description: The UCSC bed graph
pattern: "*.bedGraph.gz"
- peaks:
type: file
description: The found peaks
pattern: "*.peaks.txt"
- bed:
type: file
description: A BED file of the found peaks
pattern: "*.bed"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"

30
tests/config/pytest_modules.yml
View file

@ -214,6 +214,10 @@ biobambam/bammarkduplicates2:
- modules/biobambam/bammarkduplicates2/**
- tests/modules/biobambam/bammarkduplicates2/**
biobambam/bamsormadup:
- modules/biobambam/bamsormadup/**
- tests/modules/biobambam/bamsormadup/**
biscuit/align:
- modules/biscuit/index/**
- modules/biscuit/align/**
@ -391,9 +395,9 @@ cellranger/mkref:
- modules/cellranger/gtf/**
- tests/modules/cellranger/gtf/**
centrifuge:
- modules/centrifuge/**
- tests/modules/centrifuge/**
centrifuge/centrifuge:
- modules/centrifuge/centrifuge/**
- tests/modules/centrifuge/centrifuge/**
checkm/lineagewf:
- modules/checkm/lineagewf/**
@ -1339,6 +1343,10 @@ picard/createsequencedictionary:
- modules/picard/createsequencedictionary/**
- tests/modules/picard/createsequencedictionary/**
picard/crosscheckfingerprints:
- modules/picard/crosscheckfingerprints/**
- tests/modules/picard/crosscheckfingerprints/**
picard/filtersamreads:
- modules/picard/filtersamreads/**
- tests/modules/picard/filtersamreads/**
@ -1347,6 +1355,10 @@ picard/fixmateinformation:
- modules/picard/fixmateinformation/**
- tests/modules/picard/fixmateinformation/**
picard/liftovervcf:
- modules/picard/liftovervcf/**
- tests/modules/picard/liftovervcf/**
picard/markduplicates:
- modules/picard/markduplicates/**
- tests/modules/picard/markduplicates/**
@ -1407,6 +1419,10 @@ preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**
prinseqplusplus:
- modules/prinseqplusplus/**
- tests/modules/prinseqplusplus/**
prodigal:
- modules/prodigal/**
- tests/modules/prodigal/**
@ -1651,6 +1667,10 @@ sistr:
- modules/sistr/**
- tests/modules/sistr/**
snapaligner/index:
- modules/snapaligner/index/**
- tests/modules/snapaligner/index/**
snpdists:
- modules/snpdists/**
- tests/modules/snpdists/**
@ -1691,6 +1711,10 @@ ssuissero:
- modules/ssuissero/**
- tests/modules/ssuissero/**
stadeniolib/scramble:
- modules/stadeniolib/scramble/**
- tests/modules/stadeniolib/scramble/**
staphopiasccmec:
- modules/staphopiasccmec/**
- tests/modules/staphopiasccmec/**

1
tests/config/test_data.config
View file

@ -161,6 +161,7 @@ params {
gnomad_r2_1_1_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/gnomAD.r2.1.1.vcf.gz.tbi"
mills_and_1000g_indels_21_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz"
mills_and_1000g_indels_21_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/mills_and_1000G.indels.hg38.vcf.gz.tbi"
haplotype_map = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/germlineresources/haplotype_map.txt"
index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"

26
tests/modules/adapterremoval/test.yml
View file

@ -3,10 +3,10 @@
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
md5sum: 2fd3d5d703b63ba33a83021fccf25f77
- path: output/adapterremoval/test.truncated.gz
- path: output/adapterremoval/test.truncated.fastq.gz
md5sum: 62139afee94defad5b83bdd0b8475a1f
- path: output/adapterremoval/versions.yml
md5sum: ac5b46719719b7ee62739530b80869fc
@ -16,12 +16,12 @@
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
md5sum: b8a451d3981b327f3fdb44f40ba2d6d1
- path: output/adapterremoval/test.pair1.truncated.gz
- path: output/adapterremoval/test.pair1.truncated.fastq.gz
md5sum: 294a6277f0139bd597e57c6fa31f39c7
- path: output/adapterremoval/test.pair2.truncated.gz
- path: output/adapterremoval/test.pair2.truncated.fastq.gz
md5sum: de7b38e2c881bced8671acb1ab452d78
- path: output/adapterremoval/versions.yml
md5sum: fa621c887897da5a379c719399c17db7
@ -31,15 +31,15 @@
tags:
- adapterremoval
files:
- path: output/adapterremoval/test.collapsed.gz
- path: output/adapterremoval/test.collapsed.fastq.gz
md5sum: ff956de3532599a56c3efe5369f0953f
- path: output/adapterremoval/test.collapsed.truncated.gz
- path: output/adapterremoval/test.discarded.gz
- path: output/adapterremoval/test.log
- path: output/adapterremoval/test.collapsed.truncated.fastq.gz
- path: output/adapterremoval/test.discarded.fastq.gz
- path: output/adapterremoval/test.settings
md5sum: 7f0b2328152226e46101a535cce718b3
- path: output/adapterremoval/test.pair1.truncated.gz
- path: output/adapterremoval/test.pair1.truncated.fastq.gz
md5sum: 683be19bc1c83008944b6b719bfa34e1
- path: output/adapterremoval/test.pair2.truncated.gz
- path: output/adapterremoval/test.pair2.truncated.fastq.gz
md5sum: e6548fe061f3ef86368b26da930174d0
- path: output/adapterremoval/versions.yml
md5sum: 78f589bb313c8da0147ca8ce77d7f3bf

4
tests/modules/biobambam/bammarkduplicates2/test.yml
View file

@ -5,8 +5,8 @@
- biobambam
files:
- path: output/biobambam/test.bam
md5sum: 1cf7f957eb20b4ace9f10d0cf0a0649a
md5sum: 603edff09029096ddf2bb8a3f12d7aa7
- path: output/biobambam/test.metrics.txt
md5sum: 30d6e7d90bb5df46329d4bc0144ce927
- path: output/biobambam/versions.yml
md5sum: 0d6f3137ed4515333d73c779f2c24445
md5sum: dfdf2b084655d124acac0bfb4eda86cc

15
tests/modules/biobambam/bamsormadup/main.nf Normal file
View file

@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BIOBAMBAM_BAMSORMADUP } from '../../../../modules/biobambam/bamsormadup/main.nf'
workflow test_biobambam_bamsormadup {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
]
BIOBAMBAM_BAMSORMADUP ( input, [] )
}

5
tests/modules/biobambam/bamsormadup/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

11
tests/modules/biobambam/bamsormadup/test.yml Normal file
View file

@ -0,0 +1,11 @@
- name: biobambam bamsormadup test_biobambam_bamsormadup
command: nextflow run tests/modules/biobambam/bamsormadup -entry test_biobambam_bamsormadup -c tests/config/nextflow.config
tags:
- biobambam/bamsormadup
- biobambam
files:
- path: output/biobambam/test.bam
md5sum: 243a77fb0642fd46bb16a4d3432d19dc
- path: output/biobambam/test.metrics.txt
md5sum: 1721879bea1f3888ecd33b35e6ee0e72
- path: output/biobambam/versions.yml

37
tests/modules/centrifuge/centrifuge/main.nf Normal file
View file

@ -0,0 +1,37 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
include { CENTRIFUGE_CENTRIFUGE } from '../../../../modules/centrifuge/centrifuge/main.nf'
workflow test_centrifuge_centrifuge_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
save_unaligned = true
save_aligned = false
sam_format = false
UNTAR ( db )
CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
}
workflow test_centrifuge_centrifuge_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
db = [ [], file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz', checkIfExists: true) ]
//db_name = "minigut_cf"
save_unaligned = true
save_aligned = false
sam_format = false
UNTAR ( db )
CENTRIFUGE_CENTRIFUGE ( input, UNTAR.out.untar.map{ it[1] }, save_unaligned, save_aligned, sam_format )
}

0
tests/modules/centrifuge/nextflow.config → tests/modules/centrifuge/centrifuge/nextflow.config
View file

12
tests/modules/centrifuge/test.yml → tests/modules/centrifuge/centrifuge/test.yml
View file

@ -1,20 +1,20 @@
- name: centrifuge test_centrifuge_single_end
command: nextflow run tests/modules/centrifuge -entry test_centrifuge_single_end -c tests/config/nextflow.config
- name: centrifuge centrifuge test_centrifuge_centrifuge_single_end
command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_single_end -c tests/config/nextflow.config
tags:
- centrifuge
- centrifuge/centrifuge
files:
- path: output/centrifuge/test.kreport.txt
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.unmapped.fastq.gz
- path: output/centrifuge/versions.yml
- name: centrifuge test_centrifuge_paired_end
command: nextflow run tests/modules/centrifuge -entry test_centrifuge_paired_end -c tests/config/nextflow.config
- name: centrifuge centrifuge test_centrifuge_centrifuge_paired_end
command: nextflow run tests/modules/centrifuge/centrifuge -entry test_centrifuge_centrifuge_paired_end -c tests/config/nextflow.config
tags:
- centrifuge
- centrifuge/centrifuge
files:
- path: output/centrifuge/test.kreport.txt
- path: output/centrifuge/test.report.txt
- path: output/centrifuge/test.results.txt
- path: output/centrifuge/test.unmapped.fastq.1.gz

33
tests/modules/centrifuge/main.nf
View file

@ -1,33 +0,0 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'
workflow test_centrifuge_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
db = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
save_unaligned = true
save_aligned = false
sam_format = false
CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
}
workflow test_centrifuge_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
db = file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
save_unaligned = true
save_aligned = false
sam_format = false
CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )
}

35
tests/modules/controlfreec/assesssignificance/main.nf
View file

@ -40,3 +40,38 @@ workflow test_controlfreec_assesssignificance {
sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
}
workflow test_controlfreec_assesssignificance_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
sig_in = CONTROLFREEC_FREEC.out.CNV.join(CONTROLFREEC_FREEC.out.ratio)
CONTROLFREEC_ASSESSSIGNIFICANCE ( sig_in )
}

10
tests/modules/controlfreec/assesssignificance/test.yml
View file

@ -7,4 +7,12 @@
- path: output/controlfreec/test.p.value.txt
md5sum: 44e23b916535fbc1a3f47b57fad292df
- path: output/controlfreec/versions.yml
md5sum: 0aa42fed10d61e4570fe1e0e83ffe932
- name: controlfreec assesssignificance test_controlfreec_assesssignificance_single
command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec/assesssignificance
- controlfreec
files:
- path: output/controlfreec/test.p.value.txt
- path: output/controlfreec/versions.yml

33
tests/modules/controlfreec/freec/main.nf
View file

@ -36,3 +36,36 @@ workflow test_controlfreec_freec {
[]
)
}
workflow test_controlfreec_freec_single {
input = [
[ id:'test2', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
}

16
tests/modules/controlfreec/freec/test.yml
View file

@ -20,4 +20,18 @@
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
- path: output/controlfreec/versions.yml
md5sum: 3ab250a2ab3be22628124c7c65324651
- name: controlfreec test_controlfreec_freec_single
command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec
- controlfreec/freec
files:
- path: output/controlfreec/config.txt
- path: output/controlfreec/test2_BAF.txt
- path: output/controlfreec/test2_CNVs
- path: output/controlfreec/test2_info.txt
- path: output/controlfreec/test2_ratio.BedGraph
- path: output/controlfreec/test2_ratio.txt
- path: output/controlfreec/test2_sample.cpn
- path: output/controlfreec/versions.yml

34
tests/modules/controlfreec/freec2bed/main.nf
View file

@ -39,3 +39,37 @@ workflow test_controlfreec_freec2bed {
CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
}
workflow test_controlfreec_freec2bed_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
CONTROLFREEC_FREEC2BED ( CONTROLFREEC_FREEC.out.ratio )
}

8
tests/modules/controlfreec/freec2bed/test.yml
View file

@ -6,3 +6,11 @@
files:
- path: output/controlfreec/test.bed
md5sum: abe10b7ce94ba903503e697394c17297
- name: controlfreec freec2bed test_controlfreec_freec2bed_single
command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec/freec2bed
- controlfreec
files:
- path: output/controlfreec/test.bed

34
tests/modules/controlfreec/freec2circos/main.nf
View file

@ -39,3 +39,37 @@ workflow test_controlfreec_freec2circos {
CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
}
workflow test_controlfreec_freec2circos_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
CONTROLFREEC_FREEC2CIRCOS ( CONTROLFREEC_FREEC.out.ratio )
}

8
tests/modules/controlfreec/freec2circos/test.yml
View file

@ -6,3 +6,11 @@
files:
- path: output/controlfreec/test.circos.txt
md5sum: 19cf35f2c36b46f717dc8342b8a5a645
- name: controlfreec freec2circos test_controlfreec_freec2circos_single
command: nextflow run tests/modules/controlfreec/freec2circos -entry test_controlfreec_freec2circos_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec
- controlfreec/freec2circos
files:
- path: output/controlfreec/test.circos.txt

35
tests/modules/controlfreec/makegraph/main.nf
View file

@ -40,3 +40,38 @@ workflow test_controlfreec_makegraph {
makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
CONTROLFREEC_MAKEGRAPH ( makegraph_in )
}
workflow test_controlfreec_makegraph_single {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
[],
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
[],[],[],[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
chrfiles = [ [], file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true) ]
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
makegraph_in = CONTROLFREEC_FREEC.out.ratio.join(CONTROLFREEC_FREEC.out.BAF)
CONTROLFREEC_MAKEGRAPH ( makegraph_in )
}

10
tests/modules/controlfreec/makegraph/test.yml
View file

@ -10,3 +10,13 @@
md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
- path: output/controlfreec/test_ratio.png
md5sum: 1435b29536b3b1555b4c423f8f4fb000
- name: controlfreec makegraph test_controlfreec_makegraph_single
command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph_single -c tests/config/nextflow.config -stub-run
tags:
- controlfreec
- controlfreec/makegraph
files:
- path: output/controlfreec/test_BAF.png
- path: output/controlfreec/test_ratio.log2.png
- path: output/controlfreec/test_ratio.png

14
tests/modules/picard/crosscheckfingerprints/main.nf Normal file
View file

@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_CROSSCHECKFINGERPRINTS } from '../../../../modules/picard/crosscheckfingerprints/main.nf'
workflow test_picard_crosscheckfingerprints {
input = [
[ id:'test', single_end:false ], // meta map
[file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)],
]
PICARD_CROSSCHECKFINGERPRINTS ( input,[], file(params.test_data['homo_sapiens']['genome']['haplotype_map'], checkIfExists: true))
}

5
tests/modules/picard/crosscheckfingerprints/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PICARD_CROSSCHECKFINGERPRINTS {ext.args = "--EXIT_CODE_WHEN_MISMATCH 0"}
}

8
tests/modules/picard/crosscheckfingerprints/test.yml Normal file
View file

@ -0,0 +1,8 @@
- name: "picard crosscheckfingerprints"
command: nextflow run ./tests/modules/picard/crosscheckfingerprints -entry test_picard_crosscheckfingerprints -c ./tests/config/nextflow.config -c ./tests/modules/picard/crosscheckfingerprints/nextflow.config
tags:
- "picard"
- "picard/crosscheckfingerprints"
files:
- path: "output/picard/test.crosscheck_metrics.txt"
- path: output/picard/versions.yml

17
tests/modules/picard/liftovervcf/main.nf Normal file
View file

@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PICARD_LIFTOVERVCF } from '../../../../modules/picard/liftovervcf/main.nf'
workflow test_picard_liftovervcf {
input_vcf = [ [ id:'test' ],
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true)
]
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
chain = file(params.test_data['homo_sapiens']['genome']['genome_chain_gz'], checkIfExists: true)
fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
PICARD_LIFTOVERVCF ( input_vcf, dict, chain, fasta )
}

5
tests/modules/picard/liftovervcf/nextflow.config Normal file
View file

@ -0,0 +1,5 @@
process {
ext.args = "WARN_ON_MISSING_CONTIG=true"
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

11
tests/modules/picard/liftovervcf/test.yml Normal file
View file

@ -0,0 +1,11 @@
- name: picard liftovervcf test_picard_liftovervcf
command: nextflow run tests/modules/picard/liftovervcf -entry test_picard_liftovervcf -c tests/config/nextflow.config
tags:
- picard/liftovervcf
- picard
files:
- path: output/picard/test.lifted.vcf.gz
contains:
- "chr22"
- path: output/picard/test.unlifted.vcf.gz
- path: output/picard/versions.yml

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PRINSEQPLUSPLUS } from '../../../modules/prinseqplusplus/main.nf'
workflow test_prinseqplusplus_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
PRINSEQPLUSPLUS ( input )
}
workflow test_prinseqplusplus_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
PRINSEQPLUSPLUS ( input )
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PRINSEQPLUSPLUS {
ext.args = "-lc_entropy=0.8"
}
}

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tests/modules/prinseqplusplus/test.yml Normal file
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- name: prinseqplusplus test_prinseqplusplus_single_end
command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_single_end -c tests/config/nextflow.config
tags:
- prinseqplusplus
files:
- path: output/prinseqplusplus/test.log
contains:
- "reads removed by -lc_entropy"
- path: output/prinseqplusplus/test_bad_out.fastq.gz
- path: output/prinseqplusplus/test_good_out.fastq.gz
- path: output/prinseqplusplus/versions.yml
- name: prinseqplusplus test_prinseqplusplus_paired_end
command: nextflow run tests/modules/prinseqplusplus -entry test_prinseqplusplus_paired_end -c tests/config/nextflow.config
tags:
- prinseqplusplus
files:
- path: output/prinseqplusplus/test.log
contains:
- "reads removed by -lc_entropy"
- path: output/prinseqplusplus/test_bad_out_R1.fastq.gz
- path: output/prinseqplusplus/test_bad_out_R2.fastq.gz
- path: output/prinseqplusplus/test_good_out_R1.fastq.gz
- path: output/prinseqplusplus/test_good_out_R2.fastq.gz
- path: output/prinseqplusplus/test_single_out_R1.fastq.gz
- path: output/prinseqplusplus/test_single_out_R2.fastq.gz
- path: output/prinseqplusplus/versions.yml

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SNAPALIGNER_INDEX } from '../../../../modules/snapaligner/index/main.nf'
workflow test_snapaligner_index {
SNAPALIGNER_INDEX ( file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),[],[],[])
}

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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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- name: snapaligner index test_snapaligner_index
command: nextflow run tests/modules/snapaligner/index -entry test_snapaligner_index -c tests/config/nextflow.config
tags:
- snapaligner/index
- snapaligner
files:
- path: output/snapaligner/snap/Genome
md5sum: 7e189c954142ba37460332b467e34ed4
- path: output/snapaligner/snap/GenomeIndex
md5sum: 298da8bcb1134f7b24379a792a7a46f8
- path: output/snapaligner/snap/GenomeIndexHash
- path: output/snapaligner/snap/OverflowTable
- path: output/snapaligner/versions.yml

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tests/modules/stadeniolib/scramble/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STADENIOLIB_SCRAMBLE } from '../../../../modules/stadeniolib/scramble/main.nf'
workflow test_stadeniolib {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
STADENIOLIB_SCRAMBLE ( input, file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true), [])
}

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tests/modules/stadeniolib/scramble/nextflow.config Normal file
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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

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tests/modules/stadeniolib/scramble/test.yml Normal file
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- name: stadeniolib test_stadeniolib
command: nextflow run tests/modules/stadeniolib -entry test_stadeniolib -c tests/config/nextflow.config
tags:
- stadeniolib
files:
- path: output/stadeniolib/test.cram
- path: output/stadeniolib/versions.yml

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tests/subworkflows/nf-core/homer/groseq/main.nf Normal file
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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HOMER_GROSEQ as HOMER_GROSEQ_BAM
HOMER_GROSEQ as HOMER_GROSEQ_BED } from '../../../../../subworkflows/nf-core/homer/groseq/main'
workflow test_homer_groseq_bam {
def input = []
input = [[ id: 'test' ],
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
HOMER_GROSEQ_BAM ( input, fasta )
}
workflow test_homer_groseq_bed {
def input = []
input = [[ id: 'test' ],
[ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]]
def fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
HOMER_GROSEQ_BED ( input, fasta )
}

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tests/subworkflows/nf-core/homer/groseq/nextflow.config Normal file
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process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: '.*:HOMER_GROSEQ_BED:HOMER_MAKETAGDIRECTORY' {
ext.args = "-checkGC -format bed"
}
}

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tests/subworkflows/nf-core/homer/groseq/test.yml Normal file
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- name: subworkflow homer_groseq bam
command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bam -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
tags:
- homer
files:
- path: output/homer/test.bed
md5sum: 8d40034dfe22c5cf973071aa1e8d3617
- path: output/homer/test.bedGraph.gz
md5sum: de2b2f8ab90a909b8bfbe755bdaba407
- path: output/homer/test.peaks.txt
md5sum: 8d40034dfe22c5cf973071aa1e8d3617
- path: output/homer/versions.yml
md5sum: c85dee03f1afabe406a87743a4c5506d
- name: subworkflow homer_groseq bed
command: nextflow run ./tests/subworkflows/nf-core/homer/groseq/ -entry test_homer_groseq_bed -c tests/config/nextflow.config -c tests/subworkflows/nf-core/homer/groseq/nextflow.config
tags:
- homer
files:
- path: output/homer/test.bed
md5sum: 25e8b64946012d1c4567a04062e90fae
- path: output/homer/test.bedGraph.gz
md5sum: 2d2d1c2d3242ff74c7a922695accb9d2
- path: output/homer/test.peaks.txt
md5sum: 25e8b64946012d1c4567a04062e90fae
- path: output/homer/versions.yml
md5sum: c9b5f1248d28c216b000cba8da738455