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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-03-26 19:40:07 +01:00 committed by GitHub
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78 changed files with 1514 additions and 170 deletions
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6
modules/bakta/main.nf
View file

@ -2,10 +2,10 @@ process BAKTA {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bakta=1.3.1" : null)
conda (params.enable_conda ? "bioconda::bakta=1.4.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' :
'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/bakta:1.4.0--pyhdfd78af_1' :
'quay.io/biocontainers/bakta:1.4.0--pyhdfd78af_1' }"
input:
tuple val(meta), path(fasta)

2
modules/bakta/meta.yml
View file

@ -78,7 +78,7 @@ output:
pattern: "*.ffn"
- hypotheticals_tsv:
type: file
description: further information on hypothetical protein CDS as simple human readble tab separated values
description: additional information on hypothetical protein CDS as simple human readble tab separated values
pattern: "*.hypotheticals.tsv"
- hypotheticals_faa:
type: file

39
modules/bbmap/pileup/main.nf Normal file
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@ -0,0 +1,39 @@
process BBMAP_PILEUP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::bbmap=38.92 bioconda::samtools=1.13 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' :
'quay.io/biocontainers/mulled-v2-008daec56b7aaf3f162d7866758142b9f889d690:f5f55fc5623bb7b3f725e8d2f86bedacfd879510-0' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.stats.txt"), emit: covstats
tuple val(meta), path("*.hist.txt") , emit: hist
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
pileup.sh \\
-Xmx${task.memory.toGiga()}g \\
in=${bam} \\
out=${prefix}.coverage.stats.txt \\
hist=${prefix}.coverage.hist.txt \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bbmap: \$(bbversion.sh)
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
END_VERSIONS
"""
}

47
modules/bbmap/pileup/meta.yml Normal file
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@ -0,0 +1,47 @@
name: "bbmap_pileup"
description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file.
keywords:
- fasta
- genome
- coverage
tools:
- bbmap:
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh"
doi: ""
licence: ["UC-LBL license (see package)"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- stats:
type: file
description: Per-scaffold coverage info
pattern: "*.stats.txt"
- hist:
type: file
description: "Histogram of # occurrences of each depth level"
pattern: "*.hist.txt"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"

20
modules/cat/cat/main.nf
View file

@ -1,4 +1,5 @@
process CAT_CAT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "conda-forge::pigz=2.3.4" : null)
@ -7,12 +8,11 @@ process CAT_CAT {
'quay.io/biocontainers/pigz:2.3.4' }"
input:
path files_in
val file_out
tuple val(meta), path(files_in)
output:
path "${file_out}*" , emit: file_out
path "versions.yml" , emit: versions
tuple val(meta), path("${prefix}"), emit: file_out
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -29,16 +29,18 @@ process CAT_CAT {
// | gzipped | ungzipped | zcat | |
// | ungzipped | gzipped | cat | pigz |
def in_zip = file_list[0].endsWith('.gz')
def out_zip = file_out.endsWith('.gz')
def command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
def command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
// Use input file ending as default
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
out_zip = prefix.endsWith('.gz')
in_zip = file_list[0].endsWith('.gz')
command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
"""
$command1 \\
$args \\
${file_list.join(' ')} \\
$command2 \\
> $file_out
> ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

9
modules/cat/cat/meta.yml
View file

@ -12,13 +12,15 @@ tools:
tool_dev_url: None
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- files_in:
type: file
description: List of compressed / uncompressed files
pattern: "*"
- file_out:
type: value
description: Full name of output file with or without .gz extension
output:
- versions:
@ -32,3 +34,4 @@ output:
authors:
- "@erikrikarddaniel"
- "@FriederikeHanssen"

33
modules/controlfreec/assesssignificance/main.nf Normal file
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@ -0,0 +1,33 @@
process CONTROLFREEC_ASSESSSIGNIFICANCE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
input:
tuple val(meta), path(cnvs), path(ratio)
output:
tuple val(meta), path("*.p.value.txt"), emit: p_value_txt
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}"
"""
cat /usr/local/bin/assess_significance.R | R --slave --args ${cnvs} ${ratio}
mv *.p.value.txt ${prefix}.p.value.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

50
modules/controlfreec/assesssignificance/meta.yml Normal file
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@ -0,0 +1,50 @@
name: controlfreec_assesssignificance
description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC
keywords:
- cna
- cnv
- somatic
- single
- tumor-only
tools:
- controlfreec/assesssignificance:
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: http://boevalab.inf.ethz.ch/FREEC
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
tool_dev_url: https://github.com/BoevaLab/FREEC/
doi: "10.1093/bioinformatics/btq635"
licence: ["GPL >=2"]
input:
# Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- cnvs:
type: file
description: _CNVs file generated by FREEC
pattern: "*._CNVs"
- ratio:
type: file
description: ratio file generated by FREEC
pattern: "*.ratio.txt"
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"
- p_value_txt:
type: file
description: CNV file containing p_values for each call
pattern: "*.p.value.txt"
authors:
- "@FriederikeHanssen"

2
modules/controlfreec/main.nf → modules/controlfreec/freec/main.nf
View file

@ -1,4 +1,4 @@
process CONTROLFREEC {
process CONTROLFREEC_FREEC {
tag "$meta.id"
label 'process_low'

4
modules/controlfreec/meta.yml → modules/controlfreec/freec/meta.yml
View file

@ -1,4 +1,4 @@
name: controlfreec
name: controlfreec_freec
description: Copy number and genotype annotation from whole genome and whole exome sequencing data
keywords:
- cna
@ -7,7 +7,7 @@ keywords:
- single
- tumor-only
tools:
- controlfreec:
- controlfreec/freec:
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: http://boevalab.inf.ethz.ch/FREEC
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html

31
modules/controlfreec/freec2bed/main.nf Normal file
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@ -0,0 +1,31 @@
process CONTROLFREEC_FREEC2BED {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
input:
tuple val(meta), path(ratio)
output:
tuple val(meta), path("*.bed"), emit: bed
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}"
"""
freec2bed.pl -f ${ratio} ${args} > ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
controlfreec: \$(echo \$(freec -version 2>&1) | sed 's/^.*Control-FREEC //; s/:.*\$//' | sed -e "s/Control-FREEC v//g" )
END_VERSIONS
"""
}

45
modules/controlfreec/freec2bed/meta.yml Normal file
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@ -0,0 +1,45 @@
name: controlfreec_freec2bed
description: Plot Freec output
keywords:
- cna
- cnv
- somatic
- single
- tumor-only
tools:
- controlfreec:
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: http://boevalab.inf.ethz.ch/FREEC
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
tool_dev_url: https://github.com/BoevaLab/FREEC/
doi: "10.1093/bioinformatics/btq635"
licence: ["GPL >=2"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ratio:
type: file
description: ratio file generated by FREEC
pattern: "*.ratio.txt"
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"
- bed:
type: file
description: Bed file
pattern: "*.bed"
authors:
- "@FriederikeHanssen"

40
modules/controlfreec/makegraph/main.nf Normal file
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@ -0,0 +1,40 @@
process CONTROLFREEC_MAKEGRAPH {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::control-freec=11.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/control-freec:11.6--h1b792b2_1':
'quay.io/biocontainers/control-freec:11.6--h1b792b2_1' }"
input:
tuple val(meta), path(ratio), path(baf)
output:
tuple val(meta), path("*_BAF.png") , emit: png_baf
tuple val(meta), path("*_ratio.log2.png"), emit: png_ratio_log2
tuple val(meta), path("*_ratio.png") , emit: png_ratio
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 baf = baf ?: ""
"""
cat /usr/local/bin/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
"""
}

58
modules/controlfreec/makegraph/meta.yml Normal file
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@ -0,0 +1,58 @@
name: controlfreec_makegraph
description: Plot Freec output
keywords:
- cna
- cnv
- somatic
- single
- tumor-only
tools:
- controlfreec:
description: Copy number and genotype annotation from whole genome and whole exome sequencing data.
homepage: http://boevalab.inf.ethz.ch/FREEC
documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html
tool_dev_url: https://github.com/BoevaLab/FREEC/
doi: "10.1093/bioinformatics/btq635"
licence: ["GPL >=2"]
input:
# Only when we have meta
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- ratio:
type: file
description: ratio file generated by FREEC
pattern: "*.ratio.txt"
- baf:
type: file
description: .BAF file generated by FREEC
pattern: "*.BAF"
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"
- png_baf:
type: file
description: Image of BAF plot
pattern: "*_BAF.png"
- png_ratio_log2:
type: file
description: Image of ratio log2 plot
pattern: "*_ratio.log2.png"
- png_ratio:
type: file
description: Image of ratio plot
pattern: "*_ratio.png"
authors:
- "@FriederikeHanssen"

10
modules/deeptools/bamcoverage/main.nf
View file

@ -23,11 +23,11 @@ process DEEPTOOLS_BAMCOVERAGE {
def prefix = task.ext.prefix ?: "${meta.id}.bigWig"
"""
bamCoverage \
--bam $input \
$args \
--numberOfProcessors ${task.cpus} \
--outFileName ${prefix}
bamCoverage \\
--bam $input \\
$args \\
--numberOfProcessors ${task.cpus} \\
--outFileName ${prefix}
cat <<-END_VERSIONS > versions.yml
"${task.process}":

15
modules/dragmap/align/main.nf
View file

@ -24,16 +24,18 @@ process DRAGMAP_ALIGN {
def args = task.ext.args ?: ''
def args2 = task.ext.args2 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def read_group = meta.read_group ? "--RGSM ${meta.read_group}" : ""
def samtools_command = sort_bam ? 'sort' : 'view'
if (meta.single_end) {
"""
dragen-os \\
-r $hashmap \\
-1 $reads \\
--num-threads $task.cpus \\
$args \\
$read_group \\
--num-threads $task.cpus \\
-1 $reads \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":
@ -46,12 +48,13 @@ process DRAGMAP_ALIGN {
"""
dragen-os \\
-r $hashmap \\
$args \\
$read_group \\
--num-threads $task.cpus \\
-1 ${reads[0]} \\
-2 ${reads[1]} \\
--num-threads $task.cpus \\
$args \\
2> ${prefix}.dragmap.log \\
| samtools $samtools_command -@ $task.cpus $args2 -o ${prefix}.bam -
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
cat <<-END_VERSIONS > versions.yml
"${task.process}":

7
modules/dragonflye/main.nf
View file

@ -2,10 +2,10 @@ process DRAGONFLYE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::dragonflye=1.0.4" : null)
conda (params.enable_conda ? "bioconda::dragonflye=1.0.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/dragonflye:1.0.4--hdfd78af_0' :
'quay.io/biocontainers/dragonflye:1.0.4--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/dragonflye:1.0.11--hdfd78af_0' :
'quay.io/biocontainers/dragonflye:1.0.11--hdfd78af_0' }"
input:
tuple val(meta), path(reads)
@ -32,6 +32,7 @@ process DRAGONFLYE {
--ram $memory \\
--outdir ./ \\
--force
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dragonflye: \$(dragonflye --version 2>&1 | sed 's/^.*dragonflye //' )

4
modules/homer/findpeaks/main.nf
View file

@ -13,8 +13,8 @@ process HOMER_FINDPEAKS {
tuple val(meta), path(tagDir)
output:
tuple val(meta), path("*peaks.txt"), emit: txt
path "versions.yml" , emit: versions
tuple val(meta), path("*.peaks.txt"), emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when

6
modules/homer/findpeaks/meta.yml
View file

@ -7,7 +7,9 @@ tools:
- homer:
description: |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
documentation: http://homer.ucsd.edu/homer/
homepage: "http://homer.ucsd.edu/homer/index.html"
documentation: "http://homer.ucsd.edu/homer/"
tool_dev_url: "http://homer.ucsd.edu/homer/ngs/peaks.html"
doi: 10.1016/j.molcel.2010.05.004.
licence: ["GPL-3.0-or-later"]
input:
@ -29,7 +31,7 @@ output:
- peaks:
type: file
description: The found peaks
pattern: "*peaks.txt"
pattern: "*.peaks.txt"
- versions:
type: file
description: File containing software versions

13
modules/homer/maketagdirectory/main.nf
View file

@ -4,13 +4,13 @@ process HOMER_MAKETAGDIRECTORY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' :
'quay.io/biocontainers/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' }"
input:
tuple val(meta), path(bed)
tuple val(meta), path(bam)
path fasta
output:
@ -26,13 +26,14 @@ process HOMER_MAKETAGDIRECTORY {
"""
makeTagDirectory \\
tag_dir \\
-genome $fasta \\
$args \\
$bed \\
-genome $fasta
$bam
cat <<-END_VERSIONS > versions.yml
"${task.process}":
homer: $VERSION
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}

33
modules/homer/maketagdirectory/meta.yml
View file

@ -3,6 +3,8 @@ description: Create a tag directory with the HOMER suite
keywords:
- peaks
- bed
- bam
- sam
tools:
- homer:
description: |
@ -10,16 +12,41 @@ tools:
documentation: http://homer.ucsd.edu/homer/
doi: 10.1016/j.molcel.2010.05.004.
licence: ["GPL-3.0-or-later"]
- samtools:
description: |
SAMtools is a set of utilities for interacting with and post-processing
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
These files are generated as output by short read aligners like BWA.
homepage: http://www.htslib.org/
documentation: hhttp://www.htslib.org/doc/samtools.html
doi: 10.1093/bioinformatics/btp352
licence: ["MIT"]
- DESeq2:
description: |
Differential gene expression analysis based on the negative binomial distribution
homepage: "https://bioconductor.org/packages/DESeq2"
documentation: "https://bioconductor.org/packages/DESeq2"
tool_dev_url: "https://github.com/mikelove/DESeq2"
doi: 10.18129/B9.bioc.DESeq2
licence: ["LGPL-3.0-or-later"]
- edgeR:
description: |
Empirical Analysis of Digital Gene Expression Data in R
homepage: "https://bioinf.wehi.edu.au/edgeR"
documentation: "https://bioconductor.org/packages/edgeR"
tool_dev_url: " https://git.bioconductor.org/packages/edgeR"
doi: 10.18129/B9.bioc.edgeR
licence: ["GPL >=2"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
- bam:
type: file
description: The peak files in bed format
pattern: "*.bed"
description: BAM/BED/SAM file
pattern: "*.{bam,bed,sam}"
- fasta:
type: file
description: Fasta file of reference genome

6
modules/homer/makeucscfile/main.nf
View file

@ -13,8 +13,8 @@ process HOMER_MAKEUCSCFILE {
tuple val(meta), path(tagDir)
output:
tuple val(meta), path("tag_dir/*ucsc.bedGraph.gz"), emit: bedGraph
path "versions.yml" , emit: versions
tuple val(meta), path("*.bedGraph.gz"), emit: bedGraph
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -25,7 +25,7 @@ process HOMER_MAKEUCSCFILE {
"""
makeUCSCfile \\
$tagDir \\
-o auto \\
-o ${prefix}.bedGraph \\
$args
cat <<-END_VERSIONS > versions.yml

2
modules/homer/makeucscfile/meta.yml
View file

@ -30,7 +30,7 @@ output:
- bedGraph:
type: file
description: The UCSC bed graph
pattern: "tag_dir/*ucsc.bedGraph.gz"
pattern: "*.bedGraph.gz"
- versions:
type: file
description: File containing software versions

33
modules/homer/pos2bed/main.nf Normal file
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@ -0,0 +1,33 @@
def VERSION = '4.11' // Version information not provided by tool on CLI
process HOMER_POS2BED {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::homer=4.11" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
input:
tuple val(meta), path(peaks)
output:
tuple val(meta), path("*.bed"), emit: bed
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}"
"""
pos2bed.pl $peaks > ${prefix}.bed
cat <<-END_VERSIONS > versions.yml
"${task.process}":
homer: $VERSION
END_VERSIONS
"""
}

42
modules/homer/pos2bed/meta.yml Normal file
View file

@ -0,0 +1,42 @@
name: "homer_pos2bed"
description: Coverting from HOMER peak to BED file formats
keywords:
- peaks
tools:
- "homer":
description: |
HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
homepage: "http://homer.ucsd.edu/homer/index.html"
documentation: "http://homer.ucsd.edu/homer/"
tool_dev_url: "http://homer.ucsd.edu/homer/ngs/miscellaneous.html"
doi: 10.1016/j.molcel.2010.05.004.
licence: ["GPL-3.0-or-later"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- tagDir:
type: directory
description: "The 'Tag Directory'"
pattern: "tagDir"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: BED file
pattern: "*.bed"
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
authors:
- "@Emiller88"

36
modules/panaroo/run/main.nf Normal file
View file

@ -0,0 +1,36 @@
process PANAROO_RUN {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::panaroo=1.2.9" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/panaroo:1.2.9--pyhdfd78af_0':
'quay.io/biocontainers/panaroo:1.2.9--pyhdfd78af_0' }"
input:
tuple val(meta), path(gff)
output:
tuple val(meta), path("results/*") , emit: results
tuple val(meta), path("results/core_gene_alignment.aln"), optional: true, emit: aln
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}"
"""
panaroo \\
$args \\
-t $task.cpus \\
-o results \\
-i $gff
cat <<-END_VERSIONS > versions.yml
"${task.process}":
panaroo: \$(echo \$(panaroo --version 2>&1) | sed 's/^.*panaroo //' ))
END_VERSIONS
"""
}

47
modules/panaroo/run/meta.yml Normal file
View file

@ -0,0 +1,47 @@
name: "panaroo_run"
description: A fast and scalable tool for bacterial pangenome analysis
keywords:
- gff
- pan-genome
- alignment
tools:
- "panaroo":
description: "panaroo - an updated pipeline for pangenome investigation"
homepage: "https://gtonkinhill.github.io/panaroo/#/"
documentation: "https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart"
tool_dev_url: "https://github.com/gtonkinhill/panaroo"
doi: "10.1186/s13059-020-02090-4"
licence: "['MIT']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- gff:
type: file
description: A set of GFF3 formatted files
pattern: "*.{gff}"
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"
- results:
type: directory
description: Directory containing Panaroo result files
pattern: "*/*"
- aln:
type: file
description: Core-genome alignment produced by Panaroo (Optional)
pattern: "*.{fasta}"
authors:
- "@rpetit3"

6
modules/pirate/main.nf
View file

@ -2,10 +2,10 @@ process PIRATE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pirate=1.0.4" : null)
conda (params.enable_conda ? "bioconda::pirate=1.0.4 bioconda::perl-bioperl=1.7.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_1' :
'quay.io/biocontainers/pirate:1.0.4--hdfd78af_1' }"
'https://depot.galaxyproject.org/singularity/pirate:1.0.4--hdfd78af_2' :
'quay.io/biocontainers/pirate:1.0.4--hdfd78af_2' }"
input:
tuple val(meta), path(gff)

40
modules/preseq/ccurve/main.nf Normal file
View file

@ -0,0 +1,40 @@
process PRESEQ_CCURVE {
tag "$meta.id"
label 'process_medium'
label 'error_ignore'
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.c_curve.txt"), emit: c_curve
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}"
def paired_end = meta.single_end ? '' : '-pe'
"""
preseq \\
c_curve \\
$args \\
$paired_end \\
-output ${prefix}.c_curve.txt \\
$bam
cp .command.err ${prefix}.command.log
cat <<-END_VERSIONS > versions.yml
"${task.process}":
preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
"""
}

48
modules/preseq/ccurve/meta.yml Normal file
View file

@ -0,0 +1,48 @@
name: preseq_ccurve
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
keywords:
- preseq
- library
- complexity
tools:
- preseq:
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
homepage: http://smithlabresearch.org/software/preseq/
documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
tool_dev_url: https://github.com/smithlabcode/preseq
doi: ""
licence: ["GPL"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
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"
- ccurve:
type: file
description: File containing output of Preseq c curve
pattern: "*.{c_curve.txt}"
- log:
type: file
description: Log file containing stderr produced by Preseq
pattern: "*.{log}"
authors:
- "@drpatelh"
- "@Emiller88"

12
modules/preseq/lcextrap/main.nf
View file

@ -5,16 +5,16 @@ process PRESEQ_LCEXTRAP {
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1' :
'quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1' }"
'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h445547b_2':
'quay.io/biocontainers/preseq:3.1.2--h445547b_2' }"
input:
tuple val(meta), path(bam)
output:
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
@ -28,7 +28,7 @@ process PRESEQ_LCEXTRAP {
lc_extrap \\
$args \\
$paired_end \\
-output ${prefix}.ccurve.txt \\
-output ${prefix}.lc_extrap.txt \\
$bam
cp .command.err ${prefix}.command.log

9
modules/preseq/lcextrap/meta.yml
View file

@ -8,8 +8,8 @@ tools:
- preseq:
description: Software for predicting library complexity and genome coverage in high-throughput sequencing
homepage: http://smithlabresearch.org/software/preseq/
documentation: None
tool_dev_url: None
documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf
tool_dev_url: https://github.com/smithlabcode/preseq
doi: ""
licence: ["GPL"]
@ -34,10 +34,10 @@ output:
type: file
description: File containing software versions
pattern: "versions.yml"
- ccurve:
- lc_extrap:
type: file
description: File containing output of Preseq lcextrap
pattern: "*.{ccurve.txt}"
pattern: "*.{lc_extrap.txt}"
- log:
type: file
description: Log file containing stderr produced by Preseq
@ -45,3 +45,4 @@ output:
authors:
- "@drpatelh"
- "@Emiller88"

5
modules/samtools/mpileup/main.nf
View file

@ -8,7 +8,7 @@ process SAMTOOLS_MPILEUP {
'quay.io/biocontainers/samtools:1.15--h1170115_1' }"
input:
tuple val(meta), path(bam)
tuple val(meta), path(input), path(intervals)
path fasta
output:
@ -21,12 +21,13 @@ process SAMTOOLS_MPILEUP {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def intervals = intervals ? "-l ${intervals}" : ""
"""
samtools mpileup \\
--fasta-ref $fasta \\
--output ${prefix}.mpileup \\
$args \\
$bam
$input
cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

6
modules/samtools/mpileup/meta.yml
View file

@ -21,7 +21,7 @@ input:
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
- input:
type: file
description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}"
@ -29,6 +29,10 @@ input:
type: file
description: FASTA reference file
pattern: "*.{fasta,fa}"
- intervals:
type: file
description: Interval FILE
pattern: "*.bed"
output:
- meta:
type: map

46
tests/config/pytest_modules.yml
View file

@ -106,6 +106,10 @@ bbmap/index:
- modules/bbmap/index/**
- tests/modules/bbmap/index/**
bbmap/pileup:
- modules/bbmap/pileup/**
- tests/modules/bbmap/pileup/**
bcftools/annotate:
- modules/bcftools/annotate/**
- tests/modules/bcftools/annotate/**
@ -415,9 +419,21 @@ cnvkit/batch:
- modules/cnvkit/batch/**
- tests/modules/cnvkit/batch/**
controlfreec:
- modules/controlfreec/**
- tests/modules/controlfreec/**
controlfreec/assesssignificance:
- modules/controlfreec/assesssignificance/**
- tests/modules/controlfreec/assesssignificance/**
controlfreec/freec:
- modules/controlfreec/freec/**
- tests/modules/controlfreec/freec/**
controlfreec/freec2bed:
- modules/controlfreec/freec2bed/**
- tests/modules/controlfreec/freec2bed/**
controlfreec/makegraph:
- modules/controlfreec/makegraph/**
- tests/modules/controlfreec/makegraph/**
cooler/cload:
- modules/cooler/cload/**
@ -872,6 +888,7 @@ homer/annotatepeaks:
homer/findpeaks:
- modules/homer/findpeaks/**
- modules/homer/maketagdirectory/**
- tests/modules/homer/findpeaks/**
homer/maketagdirectory:
@ -882,6 +899,12 @@ homer/makeucscfile:
- modules/homer/makeucscfile/**
- tests/modules/homer/makeucscfile/**
homer/pos2bed:
- modules/homer/pos2bed/**
- modules/homer/maketagdirectory/**
- modules/homer/findpeaks/**
- tests/modules/homer/pos2bed/**
hpsuissero:
- modules/hpsuissero/**
- tests/modules/hpsuissero/**
@ -1244,6 +1267,10 @@ pairtools/sort:
- modules/pairtools/sort/**
- tests/modules/pairtools/sort/**
panaroo/run:
- modules/panaroo/run/**
- tests/modules/panaroo/run/**
pangolin:
- modules/pangolin/**
- tests/modules/pangolin/**
@ -1352,6 +1379,10 @@ porechop:
- modules/porechop/**
- tests/modules/porechop/**
preseq/ccurve:
- modules/preseq/ccurve/**
- tests/modules/preseq/ccurve/**
preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**
@ -1748,6 +1779,15 @@ ultra/pipeline:
- modules/ultra/pipeline/**
- tests/modules/ultra/pipeline/**
umitools/dedup:
- modules/umitools/dedup/**
- modules/umitools/extract/**
- tests/modules/umitools/dedup/**
umitools/extract:
- modules/umitools/extract/**
- tests/modules/umitools/extract/**
unicycler:
- modules/unicycler/**
- tests/modules/unicycler/**

11
tests/modules/bakta/test.yml
View file

@ -1,25 +1,14 @@
## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml bakta
- name: bakta
command: nextflow run ./tests/modules/bakta -entry test_bakta -c tests/config/nextflow.config -stub-run
tags:
- bakta
files:
- path: output/bakta/test.embl
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.faa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.ffn
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.fna
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.gbff
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.gff3
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.hypotheticals.tsv
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.hypotheticals.faa
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/bakta/test.tsv
md5sum: d41d8cd98f00b204e9800998ecf8427e

15
tests/modules/bbmap/pileup/main.nf Normal file
View file

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

5
tests/modules/bbmap/pileup/nextflow.config Normal file
View file

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

12
tests/modules/bbmap/pileup/test.yml Normal file
View file

@ -0,0 +1,12 @@
- name: "bbmap pileup"
command: nextflow run ./tests/modules/bbmap/pileup -entry test_bbmap_pileup -c ./tests/config/nextflow.config -c ./tests/modules/bbmap/pileup/nextflow.config
tags:
- "bbmap"
- "bbmap/pileup"
files:
- path: "output/bbmap/test.coverage.stats.txt"
md5sum: c3fc9d0681589b69e3301ca3cb27b7a4
- path: "output/bbmap/test.coverage.hist.txt"
md5sum: 96915920ef42ddc9483457dd4585a088
- path: output/bbmap/versions.yml
md5sum: 894acc38bdc167dc22851df15e5a8453

37
tests/modules/cat/cat/main.nf
View file

@ -2,53 +2,60 @@
nextflow.enable.dsl = 2
include { CAT_CAT } from '../../../../modules/cat/cat/main.nf'
include { CAT_CAT } from '../../../../modules/cat/cat/main.nf'
include { CAT_CAT as CAT_UNZIPPED_ZIPPED } from '../../../../modules/cat/cat/main.nf'
include { CAT_CAT as CAT_ZIPPED_UNZIPPED } from '../../../../modules/cat/cat/main.nf'
workflow test_cat_unzipped_unzipped {
input = [
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
[ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ]
]
CAT_CAT ( input, 'cat.txt' )
CAT_CAT ( input )
}
workflow test_cat_zipped_zipped {
input = [
file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
[ id:'test', single_end:true ], // meta map
[file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
]
CAT_CAT ( input, 'cat.txt.gz' )
CAT_CAT ( input )
}
workflow test_cat_zipped_unzipped {
input = [
file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)
[ id:'test', single_end:true ], // meta map
[file(params.test_data['sarscov2']['genome']['genome_gff3_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['contigs_genome_maf_gz'], checkIfExists: true)]
]
CAT_CAT ( input, 'cat.txt' )
CAT_ZIPPED_UNZIPPED ( input )
}
workflow test_cat_unzipped_zipped {
input = [
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
[ id:'test', single_end:true ], // meta map
[file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)]
]
CAT_CAT ( input, 'cat.txt.gz' )
CAT_UNZIPPED_ZIPPED ( input )
}
workflow test_cat_one_file_unzipped_zipped {
input = [
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
]
CAT_CAT ( input, 'cat.txt.gz' )
CAT_UNZIPPED_ZIPPED ( input )
}

8
tests/modules/cat/cat/nextflow.config
View file

@ -2,4 +2,12 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: CAT_UNZIPPED_ZIPPED {
ext.prefix = 'cat.txt.gz'
}
withName: CAT_ZIPPED_UNZIPPED {
ext.prefix = 'cat.txt'
}
}

4
tests/modules/cat/cat/test.yml
View file

@ -4,7 +4,7 @@
- cat
- cat/cat
files:
- path: output/cat/cat.txt
- path: output/cat/test.fasta
md5sum: f44b33a0e441ad58b2d3700270e2dbe2
- name: cat zipped zipped
@ -13,7 +13,7 @@
- cat
- cat/cat
files:
- path: output/cat/cat.txt.gz
- path: output/cat/test.gz
- name: cat zipped unzipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config

42
tests/modules/controlfreec/assesssignificance/main.nf Normal file
View file

@ -0,0 +1,42 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CONTROLFREEC_ASSESSSIGNIFICANCE } from '../../../../modules/controlfreec/assesssignificance/main.nf'
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_assesssignificance {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
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 )
}

2
tests/modules/controlfreec/nextflow.config → tests/modules/controlfreec/assesssignificance/nextflow.config
View file

@ -2,7 +2,7 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:CONTROLFREEC{
withName:CONTROLFREEC_FREEC{
ext.args = { [
"sample":[
inputformat: 'pileup',

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

@ -0,0 +1,10 @@
- name: controlfreec assesssignificance test_controlfreec_assesssignificance
command: nextflow run tests/modules/controlfreec/assesssignificance -entry test_controlfreec_assesssignificance -c tests/config/nextflow.config
tags:
- controlfreec/assesssignificance
- controlfreec
files:
- path: output/controlfreec/test.p.value.txt
md5sum: 44e23b916535fbc1a3f47b57fad292df
- path: output/controlfreec/versions.yml
md5sum: 0aa42fed10d61e4570fe1e0e83ffe932

27
tests/modules/controlfreec/main.nf → tests/modules/controlfreec/freec/main.nf
View file

@ -2,9 +2,10 @@
nextflow.enable.dsl = 2
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
include { UNTAR } from '../../../modules/untar/main.nf'
workflow test_controlfreec {
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_freec {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
@ -23,15 +24,15 @@ workflow test_controlfreec {
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
UNTAR(chrfiles)
CONTROLFREEC ( input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
CONTROLFREEC_FREEC (input,
fasta,
fai,
[],
dbsnp,
dbsnp_tbi,
UNTAR.out.untar.map{ it[1] },
[],
target_bed,
[]
)
}

26
tests/modules/controlfreec/freec/nextflow.config Normal file
View file

@ -0,0 +1,26 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:CONTROLFREEC_FREEC{
ext.args = { [
"sample":[
inputformat: 'pileup',
mateorientation: 'FR'
],
"general" :[
bedgraphoutput: "TRUE",
noisydata: "TRUE",
minexpectedgc: "0",
readcountthreshold: "1",
sex: meta.sex,
window: "10",
],
"control":[
inputformat: "pileup",
mateorientation: "FR"
]
]
}
}
}

7
tests/modules/controlfreec/test.yml → tests/modules/controlfreec/freec/test.yml
View file

@ -1,7 +1,8 @@
- name: controlfreec test_controlfreec
command: nextflow run tests/modules/controlfreec -entry test_controlfreec -c tests/config/nextflow.config
- name: controlfreec test_controlfreec_freec
command: nextflow run tests/modules/controlfreec/freec -entry test_controlfreec_freec -c tests/config/nextflow.config
tags:
- controlfreec
- controlfreec/freec
files:
- path: output/controlfreec/config.txt
- path: output/controlfreec/test.mpileup.gz_control.cpn
@ -19,4 +20,4 @@
- path: output/controlfreec/test2.mpileup.gz_sample.cpn
md5sum: c80dad58a77b1d7ba6d273999f4b4b4b
- path: output/controlfreec/versions.yml
md5sum: ff93f6466d4686aab708425782c6c848
md5sum: 3ab250a2ab3be22628124c7c65324651

41
tests/modules/controlfreec/freec2bed/main.nf Normal file
View file

@ -0,0 +1,41 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CONTROLFREEC_FREEC2BED } from '../../../../modules/controlfreec/freec2bed/main.nf'
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_freec2bed {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
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 )
}

27
tests/modules/controlfreec/freec2bed/nextflow.config Normal file
View file

@ -0,0 +1,27 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:CONTROLFREEC_FREEC{
ext.args = { [
"sample":[
inputformat: 'pileup',
mateorientation: 'FR'
],
"general" :[
bedgraphoutput: "TRUE",
noisydata: "TRUE",
minexpectedgc: "0",
readcountthreshold: "1",
sex: meta.sex,
window: "10",
],
"control":[
inputformat: "pileup",
mateorientation: "FR"
]
]
}
}
}

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

@ -0,0 +1,8 @@
- name: controlfreec freec2bed test_controlfreec_freec2bed
command: nextflow run tests/modules/controlfreec/freec2bed -entry test_controlfreec_freec2bed -c tests/config/nextflow.config
tags:
- controlfreec/freec2bed
- controlfreec
files:
- path: output/controlfreec/test.bed
md5sum: abe10b7ce94ba903503e697394c17297

42
tests/modules/controlfreec/makegraph/main.nf Normal file
View file

@ -0,0 +1,42 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { CONTROLFREEC_MAKEGRAPH } from '../../../../modules/controlfreec/makegraph/main.nf'
include { CONTROLFREEC_FREEC } from '../../../../modules/controlfreec/freec/main.nf'
include { UNTAR } from '../../../../modules/untar/main.nf'
workflow test_controlfreec_makegraph {
input = [
[ id:'test', single_end:false, sex:'XX' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
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 )
}

30
tests/modules/controlfreec/makegraph/nextflow.config Normal file
View file

@ -0,0 +1,30 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName:CONTROLFREEC_FREEC{
ext.args = { [
"sample":[
inputformat: 'pileup',
mateorientation: 'FR'
],
"general" :[
bedgraphoutput: "TRUE",
noisydata: "TRUE",
minexpectedgc: "0",
readcountthreshold: "1",
sex: meta.sex,
window: "10",
],
"control":[
inputformat: "pileup",
mateorientation: "FR"
]
]
}
}
withName:CONTROLFREEC_MAKEGRAPH {
ext.args = "2"
}
}

12
tests/modules/controlfreec/makegraph/test.yml Normal file
View file

@ -0,0 +1,12 @@
- name: controlfreec makegraph test_controlfreec_makegraph
command: nextflow run tests/modules/controlfreec/makegraph -entry test_controlfreec_makegraph -c tests/config/nextflow.config
tags:
- controlfreec
- controlfreec/makegraph
files:
- path: output/controlfreec/test_BAF.png
md5sum: f9d977839e09c7e2472d970bd4aa834c
- path: output/controlfreec/test_ratio.log2.png
md5sum: b3c7916b1b4951a0cc3da20d8e9e0262
- path: output/controlfreec/test_ratio.png
md5sum: 1435b29536b3b1555b4c423f8f4fb000

23
tests/modules/homer/maketagdirectory/main.nf
View file

@ -2,19 +2,22 @@
nextflow.enable.dsl = 2
include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
include {
HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BED
HOMER_MAKETAGDIRECTORY as HOMER_MAKETAGDIRECTORY_BAM
} from '../../../../modules/homer/maketagdirectory/main.nf'
workflow test_homer_maketagdirectory {
workflow test_homer_maketagdirectory_bed {
input = [[id:'test'],
[file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
HOMER_MAKETAGDIRECTORY (input, fasta)
HOMER_MAKETAGDIRECTORY_BED (input, fasta)
}
workflow test_homer_meta_maketagdirectory {
workflow test_homer_maketagdirectory_meta {
input =
[[[ id:'test1'],
[file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]],
@ -25,8 +28,14 @@ workflow test_homer_meta_maketagdirectory {
meta_input = [[id: 'meta_test']] + [ input.collect{it[1]}.flatten() ]
HOMER_MAKETAGDIRECTORY (meta_input, fasta)
HOMER_MAKETAGDIRECTORY_BED (meta_input, fasta)
}
// TODO Make a failing bam test
// TODO Make a pass bam test that feeds the bam through samtools first
workflow test_homer_maketagdirectory_bam {
input = [[id:'test'],
[file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)]]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
HOMER_MAKETAGDIRECTORY_BAM (input, fasta)
}

6
tests/modules/homer/maketagdirectory/nextflow.config
View file

@ -2,8 +2,12 @@ process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: HOMER_MAKETAGDIRECTORY {
withName: HOMER_MAKETAGDIRECTORY_BED {
ext.args = '-format bed'
}
withName: HOMER_MAKETAGDIRECTORY_BAM {
ext.args = '-format sam'
}
}

29
tests/modules/homer/maketagdirectory/test.yml
View file

@ -1,5 +1,5 @@
- name: homer maketagdirectory
command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
- name: homer maketagdirectory bed
command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
tags:
- homer
- homer/maketagdirectory
@ -11,12 +11,12 @@
- path: output/homer/tag_dir/tagCountDistribution.txt
md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
- path: output/homer/tag_dir/tagInfo.txt
md5sum: 816baa642c946f8284eaa465638e9abb
md5sum: ff56f30411b221b847aa4e6e9a6098a1
- path: output/homer/tag_dir/tagLengthDistribution.txt
md5sum: e5aa2b9843ca9c04ace297280aed6af4
- name: homer meta maketagdirectory
command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_meta_maketagdirectory -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
- name: homer maketagdirectory meta
command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_meta -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
tags:
- homer
- homer/maketagdirectory
@ -28,6 +28,23 @@
- path: output/homer/tag_dir/tagCountDistribution.txt
md5sum: fd4ee7ce7c5dfd7c9d739534b8180578
- path: output/homer/tag_dir/tagInfo.txt
md5sum: 816baa642c946f8284eaa465638e9abb
md5sum: ff56f30411b221b847aa4e6e9a6098a1
- path: output/homer/tag_dir/tagLengthDistribution.txt
md5sum: e5aa2b9843ca9c04ace297280aed6af4
- name: homer maketagdirectory bam
command: nextflow run ./tests/modules/homer/maketagdirectory -entry test_homer_maketagdirectory_bam -c ./tests/config/nextflow.config -c ./tests/modules/homer/maketagdirectory/nextflow.config
tags:
- homer
- homer/maketagdirectory
files:
- path: output/homer/tag_dir/MT192765.1.tags.tsv
md5sum: 365808c4751ef6dd7085ac52037a22bc
- path: output/homer/tag_dir/tagAutocorrelation.txt
md5sum: 8b396f2aef1cdd3af4fab57b142d3250
- path: output/homer/tag_dir/tagCountDistribution.txt
md5sum: afc6d007096c3872bbe84c9dc8edb832
- path: output/homer/tag_dir/tagInfo.txt
md5sum: fbaf46eeb8a0723fa8b5eabd93f9d821
- path: output/homer/tag_dir/tagLengthDistribution.txt
md5sum: 44f231adb2a705ae81950808c55cf248

2
tests/modules/homer/makeucscfile/test.yml
View file

@ -4,4 +4,4 @@
- homer
- homer/makeucscfile
files:
- path: output/homer/tag_dir/tag_dir.ucsc.bedGraph.gz
- path: output/homer/test.bedGraph.gz

19
tests/modules/homer/pos2bed/main.nf Normal file
View file

@ -0,0 +1,19 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { HOMER_MAKETAGDIRECTORY } from '../../../../modules/homer/maketagdirectory/main.nf'
include { HOMER_FINDPEAKS } from '../../../../modules/homer/findpeaks/main.nf'
include { HOMER_POS2BED } from '../../../../modules/homer/pos2bed/main.nf'
workflow test_homer_pos2bed {
input = [[id:'test'],
[file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true)]]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
HOMER_MAKETAGDIRECTORY (input, fasta)
HOMER_FINDPEAKS ( HOMER_MAKETAGDIRECTORY.out.tagdir )
HOMER_POS2BED ( HOMER_FINDPEAKS.out.txt )
}

9
tests/modules/homer/pos2bed/nextflow.config Normal file
View file

@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: HOMER_MAKETAGDIRECTORY {
ext.args = '-format bed'
}
}

10
tests/modules/homer/pos2bed/test.yml Normal file
View file

@ -0,0 +1,10 @@
- name: "homer pos2bed"
command: nextflow run ./tests/modules/homer/pos2bed -entry test_homer_pos2bed -c ./tests/config/nextflow.config -c ./tests/modules/homer/pos2bed/nextflow.config
tags:
- "homer"
- "homer/pos2bed"
files:
- path: "output/homer/test.bed"
md5sum: 0b9ebd8f06b9c820a551fbdb2d7635ee
- path: output/homer/versions.yml
md5sum: 1485f4b2d76484e8fe3310e2505de2fd

19
tests/modules/panaroo/run/main.nf Normal file
View file

@ -0,0 +1,19 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PANAROO_RUN } from '../../../../modules/panaroo/run/main.nf'
workflow test_panaroo_run {
input = [
[ id:'test', single_end:false ], // meta map
[
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test1_gff'], checkIfExists: true),
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test2_gff'], checkIfExists: true),
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
]
]
PANAROO_RUN ( input )
}

8
tests/modules/panaroo/run/nextflow.config Normal file
View file

@ -0,0 +1,8 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PANAROO_RUN {
ext.args = '--clean-mode strict -a core'
}
}

38
tests/modules/panaroo/run/test.yml Normal file
View file

@ -0,0 +1,38 @@
- name: panaroo run test_panaroo_run
command: nextflow run tests/modules/panaroo/run -entry test_panaroo_run -c tests/config/nextflow.config
tags:
- panaroo/run
- panaroo
files:
- path: output/panaroo/results/combined_DNA_CDS.fasta
md5sum: 92bd4f6b9c84c84c0989d77d2558b7d1
- path: output/panaroo/results/combined_protein_CDS.fasta
md5sum: 7a5636c4f2abc190f5dd4dfbb1da7034
- path: output/panaroo/results/combined_protein_cdhit_out.txt
md5sum: 2164b81606712b53af2198b4d50eed08
- path: output/panaroo/results/combined_protein_cdhit_out.txt.clstr
md5sum: aaa9fc2b797c932b6d9ff2df640113f1
- path: output/panaroo/results/core_alignment_header.embl
contains: ["DNA", "feature", "locus_tag"]
- path: output/panaroo/results/core_gene_alignment.aln
contains: ["test1", "test2", "test3"]
- path: output/panaroo/results/final_graph.gml
contains: ["graph", "isolateNames", "test3"]
- path: output/panaroo/results/gene_data.csv
md5sum: 45df2d26ac81754b858c0e4757e834b2
- path: output/panaroo/results/gene_presence_absence.Rtab
md5sum: 9efbed5df121dc0c4fbb58869b65c3e4
- path: output/panaroo/results/gene_presence_absence.csv
contains: ["Gene", "unique", "test3"]
- path: output/panaroo/results/gene_presence_absence_roary.csv
contains: ["Gene", "Max", "Fragment"]
- path: output/panaroo/results/pan_genome_reference.fa
md5sum: d0b03cdfaab8965d86cb1045db3c2d20
- path: output/panaroo/results/pre_filt_graph.gml
contains: ["graph", "node", "id"]
- path: output/panaroo/results/struct_presence_absence.Rtab
md5sum: 246017db1175f9b1683dfe60cb2e9b5b
- path: output/panaroo/results/summary_statistics.txt
md5sum: 9c73c416e1758bea06c67b4ec9fd0720
- path: output/panaroo/versions.yml
md5sum: 909e7b046a8a87319986d34b7328641c

4
tests/modules/pirate/main.nf
View file

@ -14,10 +14,6 @@ workflow test_pirate {
file(params.test_data['candidatus_portiera_aleyrodidarum']['genome']['test3_gff'], checkIfExists: true)
]
]
// [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
// file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
// file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
// ]
PIRATE ( input )
}

62
tests/modules/pirate/test.yml
View file

@ -16,35 +16,35 @@
- path: output/pirate/results/PIRATE.unique_alleles.tsv
contains: ["allele_name"]
- path: output/pirate/results/binary_presence_absence.fasta
contains: ["GCF_000292685"]
contains: ["test1"]
- path: output/pirate/results/binary_presence_absence.nwk
md5sum: 5b5d86bf97d97de37bb9db514abb7762
md5sum: 1fcf7434911bbab39b74791259f1f989
- path: output/pirate/results/cluster_alleles.tab
contains: ["g0001"]
- path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab
md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8
- path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab
md5sum: a24d6048b3074242bb558c7fa27a8b03
- path: output/pirate/results/co-ords/GCF_002849995.co-ords.tab
md5sum: 0c08228585f4fa95686e9b025e0fe9c1
- path: output/pirate/results/co-ords/test1.co-ords.tab
md5sum: f1e75c045b35bae260dadb1a2f000dfa
- path: output/pirate/results/co-ords/test2.co-ords.tab
md5sum: 953b0d2f1dfd4c3a6a6dd246c9174703
- path: output/pirate/results/co-ords/test3.co-ords.tab
md5sum: 61f2c52ef77dc9a97a200c57b89b7d69
- path: output/pirate/results/genome2loci.tab
md5sum: bbcea5bfcdcafe14a9aa7261c8e931b8
md5sum: 2d9cdefd5b1a7f5e20b0a70a6e5fa588
- path: output/pirate/results/genome_list.txt
md5sum: 6534b1635c258ad92b829077addc1ff5
md5sum: c19ac63da7949b15179f42093cbf95b8
- path: output/pirate/results/link_clusters.log
contains: ["parsing paralog file"]
- path: output/pirate/results/loci_list.tab
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/loci_paralog_categories.tab
md5sum: 6404d2a32526a398f42d7da768a389bd
- path: output/pirate/results/modified_gffs/GCF_000292685.gff
md5sum: 2b73bda2f84dc634303dc90e641040ca
- path: output/pirate/results/modified_gffs/GCF_000298385.gff
md5sum: b1a9d6557d47e09249f08a7acdbbd618
- path: output/pirate/results/modified_gffs/GCF_002849995.gff
md5sum: 68532fc9bb639e6d83c731a069f60cf8
md5sum: f8c3d31f445c3cb66bd95ba77be0a7b8
- path: output/pirate/results/modified_gffs/test1.gff
md5sum: 5dc220e472165c3b693e1017f38fc0e3
- path: output/pirate/results/modified_gffs/test2.gff
md5sum: 975f5c7fb363caf1be9c53e5e237bb5d
- path: output/pirate/results/modified_gffs/test3.gff
md5sum: a4735a5ac75ce82aadba8a3de6cabc2e
- path: output/pirate/results/pan_sequences.fasta
md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb
md5sum: 0492833706f0f969b49a3555c16ec40d
- path: output/pirate/results/pangenome.connected_blocks.tsv
contains: ["block_number"]
- path: output/pirate/results/pangenome.edges
@ -59,29 +59,29 @@
contains: ["g0091"]
- path: output/pirate/results/pangenome.temp
- path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output
md5sum: 9da25d27684bfcc5488987ab2d1fd3a1
md5sum: ffb3b5bf1ba24bf2bd0be677500139a2
- path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters
contains: ["GCF_000298385_00081"]
contains: ["test1_00081"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab
contains: ["GCF_000298385_00242"]
contains: ["test1_00242"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt
contains: ["chaos"]
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta
md5sum: 84668b6c65b57026a17a50b0edd02541
md5sum: 6e483c773ed90bd50b33f2bd569343e4
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pot
- path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf
@ -95,4 +95,4 @@
- path: output/pirate/results/representative_sequences.ffn
contains: ["representative_genome"]
- path: output/pirate/results/split_groups.log
contains: ["g0213"]
contains: ["g0"]

25
tests/modules/preseq/ccurve/main.nf Normal file
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@ -0,0 +1,25 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PRESEQ_CCURVE } from '../../../../modules/preseq/ccurve/main.nf'
workflow test_preseq_ccurve_single_end {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
PRESEQ_CCURVE ( input )
}
workflow test_preseq_ccurve_paired_end {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
]
PRESEQ_CCURVE ( input )
}

5
tests/modules/preseq/ccurve/nextflow.config Normal file
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@ -0,0 +1,5 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}

19
tests/modules/preseq/ccurve/test.yml Normal file
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@ -0,0 +1,19 @@
- name: preseq ccurve single-end
command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_single_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
tags:
- preseq
- preseq/ccurve
files:
- path: output/preseq/test.c_curve.txt
md5sum: cf4743abdd355595d6ec1fb3f38e66e5
- path: output/preseq/test.command.log
- name: preseq ccurve paired-end
command: nextflow run ./tests/modules/preseq/ccurve -entry test_preseq_ccurve_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/preseq/ccurve/nextflow.config
tags:
- preseq
- preseq/ccurve
files:
- path: output/preseq/test.c_curve.txt
md5sum: cf4743abdd355595d6ec1fb3f38e66e5
- path: output/preseq/test.command.log

4
tests/modules/preseq/lcextrap/test.yml
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@ -4,7 +4,7 @@
- preseq
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
- path: output/preseq/test.lc_extrap.txt
md5sum: 1fa5cdd601079329618f61660bee00de
- path: output/preseq/test.command.log
@ -14,6 +14,6 @@
- preseq
- preseq/lcextrap
files:
- path: output/preseq/test.ccurve.txt
- path: output/preseq/test.lc_extrap.txt
md5sum: 10e5ea860e87fb6f5dc10f4f20c62040
- path: output/preseq/test.command.log

13
tests/modules/samtools/mpileup/main.nf
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@ -6,7 +6,18 @@ include { SAMTOOLS_MPILEUP } from '../../../../modules/samtools/mpileup/main.nf'
workflow test_samtools_mpileup {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
[]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
SAMTOOLS_MPILEUP ( input, fasta )
}
workflow test_samtools_mpileup_intervals {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

19
tests/modules/samtools/mpileup/test.yml
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@ -1,8 +1,21 @@
- name: samtools mpileup
command: nextflow run ./tests/modules/samtools/mpileup -entry test_samtools_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/samtools/mpileup/nextflow.config
- name: samtools mpileup test_samtools_mpileup
command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup -c tests/config/nextflow.config
tags:
- samtools
- samtools/mpileup
files:
- path: ./output/samtools/test.mpileup
- path: output/samtools/test.mpileup
md5sum: 958e6bead4103d72026f80153b6b5150
- path: output/samtools/versions.yml
md5sum: 26350e1e145451f0b807911db029861e
- name: samtools mpileup test_samtools_mpileup_intervals
command: nextflow run tests/modules/samtools/mpileup -entry test_samtools_mpileup_intervals -c tests/config/nextflow.config
tags:
- samtools
- samtools/mpileup
files:
- path: output/samtools/test.mpileup
md5sum: 958e6bead4103d72026f80153b6b5150
- path: output/samtools/versions.yml
md5sum: 11d8118a558efb9db6798453862d719c

56
tests/modules/umitools/dedup/main.nf Normal file
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@ -0,0 +1,56 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf'
include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf'
include { SAMTOOLS_INDEX } from '../../../../modules/samtools/index/main.nf'
include { UMITOOLS_DEDUP } from '../../../../modules/umitools/dedup/main.nf'
//
// Test with no UMI
//
workflow test_umitools_dedup_no_umi {
input = [ [ id:'test'], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
]
UMITOOLS_DEDUP ( input )
}
//
// Test with single-end data
//
workflow test_umitools_dedup_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
UMITOOLS_EXTRACT ( input )
BWA_INDEX ( fasta )
BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
SAMTOOLS_INDEX (BWA_MEM.out.bam)
UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
}
//
// Test with paired-end data
//
workflow test_umitools_dedup_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) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
UMITOOLS_EXTRACT ( input )
BWA_INDEX ( fasta )
BWA_MEM ( UMITOOLS_EXTRACT.out.reads, BWA_INDEX.out.index, true )
SAMTOOLS_INDEX (BWA_MEM.out.bam)
UMITOOLS_DEDUP(BWA_MEM.out.bam.join(SAMTOOLS_INDEX.out.bai, by: [0]))
}

17
tests/modules/umitools/dedup/nextflow.config Normal file
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@ -0,0 +1,17 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: UMITOOLS_EXTRACT {
ext.args = '--bc-pattern="NNNN"'
}
withName: UMITOOLS_DEDUP {
ext.args = ''
ext.prefix = 'dedup'
}
withName: BWA_MEM {
ext.args2 = ''
}
}

54
tests/modules/umitools/dedup/test.yml Normal file
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@ -0,0 +1,54 @@
- name: umitools dedup test_umitools_dedup_no_umi
command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_no_umi -c tests/config/nextflow.config
tags:
- umitools/dedup
- umitools
files:
- path: output/umitools/dedup.bam
md5sum: 53b4edc399db81b87d2343e78af73cf0
- path: output/umitools/dedup_edit_distance.tsv
md5sum: 65186b0964e2f8d970cc04d736d8b119
- path: output/umitools/dedup_per_umi.tsv
md5sum: 8e6783a4a79437b095f095f2aefe7c01
- path: output/umitools/dedup_per_umi_per_position.tsv
md5sum: 9386db4a104b8e4e32f3ca4a84efa4ac
- path: output/umitools/versions.yml
md5sum: 4aaaa33565bcd9a984255139933d6446
- name: umitools dedup test_umitools_dedup_single_end
command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_single_end -c tests/config/nextflow.config
tags:
- umitools
- umitools/dedup
files:
- path: output/bwa/test.bam
md5sum: ea41a3cdca1856b22845e1067fd31f37
- path: output/bwa/versions.yml
md5sum: ce4d987f2c53f4c01b31d210c357b24a
- path: output/samtools/test.bam.bai
md5sum: 095af0ad3921212597ffd7c342ecd5a0
- path: output/samtools/versions.yml
md5sum: 69b7cde627c9b4e8403dfc125db71cc7
- path: output/umitools/dedup.bam
md5sum: d95df177063432748ff33f473910cb1e
- path: output/umitools/versions.yml
md5sum: 730e768dd199d2f5bfb6fd0850446344
- name: umitools dedup test_umitools_dedup_paired_end
command: nextflow run tests/modules/umitools/dedup -entry test_umitools_dedup_paired_end -c tests/config/nextflow.config
tags:
- umitools
- umitools/dedup
files:
- path: output/bwa/test.bam
md5sum: 1ad786cae0ff2254c655e3a206929617
- path: output/bwa/versions.yml
md5sum: b524c5ddf61c20f4a0a93ae8fc78b851
- path: output/samtools/test.bam.bai
md5sum: 7496f4056a8e86327ca93e350f282fc2
- path: output/samtools/versions.yml
md5sum: 72fc2ab934fd4bca0f7f14a705530d34
- path: output/umitools/dedup.bam
md5sum: e8d1eae2aacef76254948c5568e94555
- path: output/umitools/versions.yml
md5sum: fd39e05042d354b3d8de49b617d3183d

29
tests/modules/umitools/extract/main.nf Normal file
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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UMITOOLS_EXTRACT } from '../../../../modules/umitools/extract/main.nf'
//
// Test with single-end data
//
workflow test_umitools_extract_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
UMITOOLS_EXTRACT ( input )
}
//
// Test with paired-end data
//
workflow test_umitools_extract_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) ]
]
UMITOOLS_EXTRACT ( input )
}

9
tests/modules/umitools/extract/nextflow.config Normal file
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@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: UMITOOLS_EXTRACT {
ext.args = '--bc-pattern="NNNN"'
}
}

27
tests/modules/umitools/extract/test.yml Normal file
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@ -0,0 +1,27 @@
- name: umitools extract test_umitools_extract_single_end
command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_single_end -c tests/config/nextflow.config
tags:
- umitools/extract
- umitools
files:
- path: output/umitools/test.umi_extract.fastq.gz
should_exist: true
- path: output/umitools/test.umi_extract.log
contains: ["job finished in"]
- path: output/umitools/versions.yml
md5sum: 397e6972343f9d7b8eae387fc18c12c7
- name: umitools extract test_umitools_extract_paired_end
command: nextflow run tests/modules/umitools/extract -entry test_umitools_extract_paired_end -c tests/config/nextflow.config
tags:
- umitools/extract
- umitools
files:
- path: output/umitools/test.umi_extract.log
contains: ["job finished in"]
- path: output/umitools/test.umi_extract_1.fastq.gz
should_exist: true
- path: output/umitools/test.umi_extract_2.fastq.gz
should_exist: true
- path: output/umitools/versions.yml
md5sum: 0aec6f919d62b7b79f6d0c5d79411464