Merge branch 'nf-core:master' into master

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FriederikeHanssen 2022-04-07 12:22:40 +02:00 committed by GitHub
commit f8b56d1248
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72 changed files with 1454 additions and 184 deletions

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@ -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")

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@ -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

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@ -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)

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@ -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
"""
}

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@ -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"

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@ -49,6 +49,8 @@ process CAT_CAT {
"""
stub:
def file_list = files_in.collect { it.toString() }
prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
"""
touch $prefix

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@ -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}":

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@ -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

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@ -4,7 +4,7 @@ process CNVPYTOR_CALLCNVS {
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
@ -30,4 +30,15 @@ process CNVPYTOR_CALLCNVS {
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}

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@ -4,7 +4,7 @@ process CNVPYTOR_HISTOGRAM {
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
@ -29,4 +29,14 @@ process CNVPYTOR_HISTOGRAM {
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
stub:
"""
touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}

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@ -4,7 +4,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
@ -35,4 +35,15 @@ process CNVPYTOR_IMPORTREADDEPTH {
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}

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@ -4,7 +4,7 @@ process CNVPYTOR_PARTITION {
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
'https://depot.galaxyproject.org/singularity/cnvpytor:1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
@ -18,7 +18,7 @@ process CNVPYTOR_PARTITION {
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: '1000'
def args = task.ext.args ?: ''
"""
cnvpytor \\
-root $pytor \\
@ -29,4 +29,14 @@ process CNVPYTOR_PARTITION {
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
stub:
"""
touch ${pytor.baseName}.pytor
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}

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@ -2,27 +2,28 @@ process DASTOOL_DASTOOL {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null)
conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/das_tool:1.1.3--r41hdfd78af_0' :
'quay.io/biocontainers/das_tool:1.1.3--r41hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
input:
tuple val(meta), path(contigs), path(bins)
path(proteins)
path(db_directory)
val(search_engine)
output:
tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("*_summary.txt") , emit: summary
tuple val(meta), path("*_DASTool_scaffolds2bin.txt") , emit: scaffolds2bin
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
tuple val(meta), path("*.proteins.faa") , optional: true, emit: fasta_proteins
tuple val(meta), path("*.candidates.faa") , optional: true, emit: fasta_proteins
tuple val(meta), path("*.faa") , optional: true, emit: candidates_faa
tuple val(meta), path("*.archaea.scg") , optional: true, emit: fasta_archaea_scg
tuple val(meta), path("*.bacteria.scg") , optional: true, emit: fasta_bacteria_scg
tuple val(meta), path("*.b6") , optional: true, emit: b6
tuple val(meta), path("*.seqlength") , optional: true, emit: seqlength
path "versions.yml" , emit: versions
@ -33,17 +34,12 @@ process DASTOOL_DASTOOL {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def bin_list = bins instanceof List ? bins.join(",") : "$bins"
def engine = search_engine ? "--search_engine $search_engine" : "--search_engine diamond"
def db_dir = db_directory ? "--db_directory $db_directory" : ""
def clean_contigs = contigs.toString() - ".gz"
def decompress_contigs = contigs.toString() == clean_contigs ? "" : "gunzip -q -f $contigs"
def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
def clean_proteins = proteins ? proteins.toString() - ".gz" : ""
def proteins_pred = proteins ? "--proteins $clean_proteins" : ""
if (! search_engine) {
log.info('[DAS_Tool] Default search engine (USEARCH) is proprietary software and not available in bioconda. Using DIAMOND as alternative.')
}
def decompress_proteins = proteins ? "gunzip -f $proteins" : ""
def proteins_pred = proteins ? "-p $clean_proteins" : ""
"""
$decompress_proteins
@ -53,15 +49,14 @@ process DASTOOL_DASTOOL {
$args \\
$proteins_pred \\
$db_dir \\
$engine \\
-t $task.cpus \\
--bins $bin_list \\
-i $bin_list \\
-c $clean_contigs \\
-o $prefix
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool version //' )
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
END_VERSIONS
"""
}

View file

@ -34,8 +34,8 @@ input:
pattern: "*.{fa.gz,fas.gz,fasta.gz}"
- bins:
type: file
description: "Scaffolds2bin tabular file generated with dastool/scaffolds2bin"
pattern: "*.scaffolds2bin.tsv"
description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin"
pattern: "*.tsv"
- proteins:
type: file
description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo)
@ -43,9 +43,6 @@ input:
- db_directory:
type: file
description: (optional) Directory of single copy gene database.
- search_engine:
type: val
description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond]
output:
- meta:
@ -65,14 +62,17 @@ output:
type: file
description: Summary of output bins including quality and completeness estimates
pattern: "*summary.txt"
- scaffolds2bin:
- contig2bin:
type: file
description: Scaffolds to bin file of output bins
pattern: "*.scaffolds2bin.txt"
pattern: "*.contig2bin.txt"
- eval:
type: file
description: Quality and completeness estimates of input bin sets
pattern: "*.eval"
- bins:
description: Final refined bins in fasta format
pattern: "*.fa"
- pdfs:
type: file
description: Plots showing the amount of high quality bins and score distribution of bins per method
@ -89,6 +89,10 @@ output:
type: file
description: Results of bacterial single-copy-gene prediction
pattern: "*.bacteria.scg"
- b6:
type: file
description: Results in b6 format
pattern: "*.b6"
- seqlength:
type: file
description: Summary of contig lengths

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@ -0,0 +1,41 @@
process DASTOOL_FASTATOCONTIG2BIN {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/das_tool:1.1.4--r41hdfd78af_1' :
'quay.io/biocontainers/das_tool:1.1.4--r41hdfd78af_1' }"
input:
tuple val(meta), path(fasta)
val(extension)
output:
tuple val(meta), path("*.tsv"), emit: fastatocontig2bin
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 file_extension = extension ? extension : "fasta"
def clean_fasta = fasta.toString() - ".gz"
def decompress_fasta = fasta.toString() == clean_fasta ? "" : "gunzip -q -f $fasta"
"""
$decompress_fasta
Fasta_to_Contig2Bin.sh \\
$args \\
-i . \\
-e $file_extension \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
dastool: \$( DAS_Tool --version 2>&1 | grep "DAS Tool" | sed 's/DAS Tool //' )
END_VERSIONS
"""
}

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@ -0,0 +1,56 @@
name: dastool_fastatocontig2bin
description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format
keywords:
- binning
- das tool
- table
- de novo
- bins
- contigs
- assembly
- das_tool
tools:
- dastool:
description: |
DAS Tool is an automated method that integrates the results
of a flexible number of binning algorithms to calculate an optimized, non-redundant
set of bins from a single assembly.
homepage: https://github.com/cmks/DAS_Tool
documentation: https://github.com/cmks/DAS_Tool
tool_dev_url: https://github.com/cmks/DAS_Tool
doi: "10.1038/s41564-018-0171-1"
licence: ["BSD"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins
pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
- extension:
type: val
description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input.
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"
- fastatocontig2bin:
type: file
description: tabular contig2bin file for DAS tool input
pattern: "*.tsv"
authors:
- "@maxibor"
- "@jfy133"

View file

@ -46,7 +46,7 @@ process DEEPVARIANT {
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.vcf.gz
touch ${prefix}.g.vcf.gz

View file

@ -39,9 +39,8 @@ process GATK4_CREATESEQUENCEDICTIONARY {
"""
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.dict
touch test.dict
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -0,0 +1,40 @@
process GSTAMA_POLYACLEANUP {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gs-tama=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gs-tama:1.0.3--hdfd78af_0':
'quay.io/biocontainers/gs-tama:1.0.3--hdfd78af_0' }"
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path("*_tama.fa.gz") , emit: fasta
tuple val(meta), path("*_tama_polya_flnc_report.txt.gz"), emit: report
tuple val(meta), path("*_tama_tails.fa.gz") , emit: tails
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$fasta" == "${prefix}.fasta" | "$fasta" == "${prefix}.fa" ) error "Input and output names are the same, set prefix in module configuration"
"""
tama_flnc_polya_cleanup.py \\
-f $fasta \\
-p ${prefix} \\
$args
gzip ${prefix}.fa
gzip ${prefix}_polya_flnc_report.txt
gzip ${prefix}_tails.fa
cat <<-END_VERSIONS > versions.yml
"${task.process}":
gstama: \$( tama_collapse.py -version | grep 'tc_version_date_'|sed 's/tc_version_date_//g' )
END_VERSIONS
"""
}

View file

@ -0,0 +1,55 @@
name: gstama_polyacleanup
description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)
keywords:
- gstama
- gstama/polyacleanup
- long-read
- isoseq
- tama
- trancriptome
- annotation
tools:
- gstama:
description: Gene-Switch Transcriptome Annotation by Modular Algorithms
homepage: https://github.com/sguizard/gs-tama
documentation: https://github.com/GenomeRIK/tama/wiki
tool_dev_url: https://github.com/sguizard/gs-tama
doi: "https://doi.org/10.1186/s12864-020-07123-7"
licence: ["GPL v3 License"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Full Length Non Chimeric reads in fasta format
pattern: "*.{fa,fasta}"
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"
- fasta:
type: file
description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip.
pattern: "*_tama.fa.gz"
- report:
type: file
description: A text file describing the number of polyA tails removed and their length. Compressed with gzip.
pattern: "*_tama_polya_flnc_report.txt.gz"
- tails:
type: file
description: A gzip compressed FASTA file of trimmed polyA tails.
pattern: "*_tama_tails.fa.gz"
authors:
- "@sguizard"

View file

@ -8,9 +8,10 @@ process MANTA_GERMLINE {
'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }"
input:
tuple val(meta), path(input), path(index), path(target_bed), path(target_bed_tbi)
tuple val(meta), path(input), path(index)
path fasta
path fasta_fai
tuple path(target_bed), path(target_bed_tbi)
output:

View file

@ -26,7 +26,7 @@ process PHANTOMPEAKQUALTOOLS {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
RUN_SPP=`which run_spp.R`
Rscript -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" -p=$task.cpus
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -0,0 +1,60 @@
name: "phantompeakqualtools"
description:
keywords:
- "ChIP-Seq"
- "QC"
- "phantom peaks"
tools:
- "phantompeakqualtools":
description: |
"This package computes informative enrichment and quality measures
for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used
to obtain robust estimates of the predominant fragment length or
characteristic tag shift values in these assays."
homepage: "None"
documentation: "https://github.com/kundajelab/phantompeakqualtools"
tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools"
doi: "https://doi.org/10.1101/gr.136184.111"
licence: "['BSD-3-clause']"
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"
- spp:
type: file
description: |
A ChIP-Seq Processing Pipeline file containing
peakshift/phantomPeak results
pattern: "*.{out}"
- pdf:
type: file
description: A pdf containing save cross-correlation plots
pattern: "*.{pdf}"
- rdata:
type: file
description: Rdata file containing the R session
pattern: "*.{Rdata}"
authors:
- "@drpatelh"
- "@Emiller88"
- "@JoseEspinosa"

View file

@ -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
"""
}
}

View file

@ -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"

View file

@ -2,10 +2,10 @@ process PYDAMAGE_ANALYZE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai)

View file

@ -2,10 +2,10 @@ process PYDAMAGE_FILTER {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::pydamage=0.62" : null)
conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/pydamage:0.62--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.62--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/pydamage:0.70--pyhdfd78af_0' :
'quay.io/biocontainers/pydamage:0.70--pyhdfd78af_0' }"
input:
tuple val(meta), path(csv)

View file

@ -0,0 +1,34 @@
process SEQKIT_STATS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0':
'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.tsv"), emit: stats
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: '--all'
def prefix = task.ext.prefix ?: "${meta.id}"
"""
seqkit stats \\
--tabular \\
$args \\
$reads > '${prefix}.tsv'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqkit: \$( seqkit version | sed 's/seqkit v//' )
END_VERSIONS
"""
}

View file

@ -0,0 +1,44 @@
name: "seqkit_stats"
description: simple statistics of FASTA/Q files
keywords:
- seqkit
- stats
tools:
- "seqkit":
description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
homepage: https://bioinf.shenwei.me/seqkit/usage/
documentation: https://bioinf.shenwei.me/seqkit/usage/
tool_dev_url: https://github.com/shenwei356/seqkit/
doi: "10.1371/journal.pone.0163962"
licence: ["MIT"]
input:
- meta:
type: map
description: >
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: >
Either FASTA or FASTQ files.
pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.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"
- stats:
type: file
description: >
Tab-separated output file with basic sequence statistics.
pattern: "*.tsv"
authors:
- "@Midnighter"

View file

@ -2,10 +2,10 @@ process SVDB_MERGE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
input:
tuple val(meta), path(vcfs)

View file

@ -2,10 +2,10 @@ process SVDB_QUERY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::svdb=2.5.2" : null)
conda (params.enable_conda ? "bioconda::svdb=2.6.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/svdb:2.5.2--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.5.2--py39h5371cbf_0' }"
'https://depot.galaxyproject.org/singularity/svdb:2.6.0--py39h5371cbf_0':
'quay.io/biocontainers/svdb:2.6.0--py39h5371cbf_0' }"
input:
tuple val(meta), path(vcf)

View file

@ -40,8 +40,8 @@ process TIDDIT_COV {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.wig
touch $prefix.tab
touch ${prefix}.wig
touch ${prefix}.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -42,9 +42,9 @@ process TIDDIT_SV {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch $prefix.vcf
touch $prefix.ploidy.tab
touch $prefix.signals.tab
touch ${prefix}.vcf
touch ${prefix}.ploidy.tab
touch ${prefix}.signals.tab
cat <<-END_VERSIONS > versions.yml
"${task.process}":

View file

@ -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 ]
}

View file

@ -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"

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/**
@ -487,6 +491,10 @@ dastool/dastool:
- modules/dastool/dastool/**
- tests/modules/dastool/dastool/**
dastool/fastatocontig2bin:
- modules/dastool/fastatocontig2bin/**
- tests/modules/dastool/fastatocontig2bin/**
dastool/scaffolds2bin:
- modules/dastool/scaffolds2bin/**
- tests/modules/dastool/scaffolds2bin/**
@ -811,6 +819,10 @@ gstama/merge:
- modules/gstama/merge/**
- tests/modules/gstama/merge/**
gstama/polyacleanup:
- modules/gstama/polyacleanup/**
- tests/modules/gstama/polyacleanup/**
gtdbtk/classifywf:
- modules/gtdbtk/classifywf/**
- tests/modules/gtdbtk/classifywf/**
@ -1299,6 +1311,10 @@ peddy:
- modules/peddy/**
- tests/modules/peddy/**
phantompeakqualtools:
- modules/phantompeakqualtools/**
- tests/modules/phantompeakqualtools/**
phyloflash:
- modules/phyloflash/**
- tests/modules/phyloflash/**
@ -1395,6 +1411,10 @@ preseq/lcextrap:
- modules/preseq/lcextrap/**
- tests/modules/preseq/lcextrap/**
prinseqplusplus:
- modules/prinseqplusplus/**
- tests/modules/prinseqplusplus/**
prodigal:
- modules/prodigal/**
- tests/modules/prodigal/**
@ -1591,6 +1611,10 @@ seqkit/split2:
- modules/seqkit/split2/**
- tests/modules/seqkit/split2/**
seqkit/stats:
- modules/seqkit/stats/**
- tests/modules/seqkit/stats/**
seqsero2:
- modules/seqsero2/**
- tests/modules/seqsero2/**

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

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

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, [] )
}

View file

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

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

View file

@ -7,6 +7,14 @@
- path: output/cat/test.fasta
md5sum: f44b33a0e441ad58b2d3700270e2dbe2
- name: cat unzipped unzipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/test.fasta
- name: cat zipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
@ -15,6 +23,14 @@
files:
- path: output/cat/test.gz
- name: cat zipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- 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
tags:
@ -24,6 +40,14 @@
- path: output/cat/cat.txt
md5sum: c439d3b60e7bc03e8802a451a0d9a5d9
- name: cat zipped unzipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_zipped_unzipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt
- name: cat unzipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
@ -32,6 +56,14 @@
files:
- path: output/cat/cat.txt.gz
- name: cat unzipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt.gz
- name: cat one file unzipped zipped
command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config
tags:
@ -39,3 +71,11 @@
- cat/cat
files:
- path: output/cat/cat.txt.gz
- name: cat one file unzipped zipped stub
command: nextflow run ./tests/modules/cat/cat -entry test_cat_one_file_unzipped_zipped -c ./tests/config/nextflow.config -c ./tests/modules/cat/cat/nextflow.config -stub-run
tags:
- cat
- cat/cat
files:
- path: output/cat/cat.txt.gz

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 )
}

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

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 )
}

View file

@ -4,7 +4,17 @@
- cnvpytor
- cnvpytor/callcnvs
files:
- path: output/cnvpytor/calls.10000.tsv
- path: output/cnvpytor/test.tsv
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/cnvpytor/versions.yml
md5sum: 5fe6ca3ef5c40f9dbf487f28db237821
md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa
- name: cnvpytor callcnvs test_cnvpytor_callcnvs stub
command: nextflow run tests/modules/cnvpytor/callcnvs -entry test_cnvpytor_callcnvs -c tests/config/nextflow.config -stub-run
tags:
- cnvpytor
- cnvpytor/callcnvs
files:
- path: output/cnvpytor/test.tsv
- path: output/cnvpytor/versions.yml
md5sum: 0bea08a253fcb2ff0ff79b99df77b9fa

View file

@ -7,4 +7,14 @@
- path: output/cnvpytor/test.pytor
md5sum: aa03a8fa15b39f77816705a48e10312a
- path: output/cnvpytor/versions.yml
md5sum: 9a4b176afd5f1a3edeb37eeb301cf464
md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2
- name: cnvpytor histogram test_cnvpytor_histogram stub
command: nextflow run tests/modules/cnvpytor/histogram -entry test_cnvpytor_histogram -c tests/config/nextflow.config -stub-run
tags:
- cnvpytor
- cnvpytor/histogram
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: 0f4d75c4f3a3eb26c22616d12b0b78b2

View file

@ -8,5 +8,5 @@ process {
}
params {
cnvpytor_chr = '' // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
cnvpytor_chr = null // specifies chromosome name(s) the same way as they are described in the sam/bam/cram header e.g. '1 2' or 'chr1 chr2'.
}

View file

@ -0,0 +1,39 @@
- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth
command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config
tags:
- cnvpytor
- cnvpytor/importreaddepth
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: 5834495324c08a37f3fd73ccdd881dc8
- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth stub
command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth -c tests/config/nextflow.config -stub-run
tags:
- cnvpytor
- cnvpytor/importreaddepth
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: 5834495324c08a37f3fd73ccdd881dc8
- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram
command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config
tags:
- cnvpytor
- cnvpytor/importreaddepth
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: dfa0afb0982d985b96d1633f71ebb82a
- name: cnvpytor importreaddepth test_cnvpytor_importreaddepth_cram stub
command: nextflow run tests/modules/cnvpytor/importreaddepth -entry test_cnvpytor_importreaddepth_cram -c tests/config/nextflow.config -stub-run
tags:
- cnvpytor
- cnvpytor/importreaddepth
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: dfa0afb0982d985b96d1633f71ebb82a

View file

@ -7,4 +7,14 @@
- path: output/cnvpytor/test.pytor
md5sum: aa03a8fa15b39f77816705a48e10312a
- path: output/cnvpytor/versions.yml
md5sum: 8a04506554c58cd170cc050fd9904c6f
md5sum: 7fd6ec952a316463bcd324f176b46b64
- name: cnvpytor partition test_cnvpytor_partition stub
command: nextflow run tests/modules/cnvpytor/partition -entry test_cnvpytor_partition -c tests/config/nextflow.config -stub-run
tags:
- cnvpytor
- cnvpytor/partition
files:
- path: output/cnvpytor/test.pytor
- path: output/cnvpytor/versions.yml
md5sum: 7fd6ec952a316463bcd324f176b46b64

View file

@ -3,7 +3,7 @@ nextflow.enable.dsl = 2
include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_SCAFFOLDS2BIN } from '../../../../modules/dastool/scaffolds2bin/main.nf'
include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
include { DASTOOL_DASTOOL } from '../../../../modules/dastool/dastool/main.nf'
workflow test_dastool_dastool {
@ -21,13 +21,13 @@ workflow test_dastool_dastool {
METABAT2_METABAT2 ( input_metabat2 )
DASTOOL_SCAFFOLDS2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
Channel.of([ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)])
.join(DASTOOL_SCAFFOLDS2BIN.out.scaffolds2bin)
.join( DASTOOL_FASTATOCONTIG2BIN.out.fastatocontig2bin )
.set {input_dastool}
DASTOOL_DASTOOL ( input_dastool, [], [], [] )
DASTOOL_DASTOOL ( input_dastool, [], [] )
}

View file

@ -1,29 +1,28 @@
- name: dastool dastool test_dastool_dastool
command: nextflow run ./tests/modules/dastool/dastool -entry test_dastool_dastool -c ./tests/config/nextflow.config -c ./tests/modules/dastool/dastool/nextflow.config
command: nextflow run tests/modules/dastool/dastool -entry test_dastool_dastool -c tests/config/nextflow.config
tags:
- dastool
- dastool/dastool
- dastool
files:
- path: output/dastool/test.seqlength
md5sum: b815a5811008c36808a59b1d0dcfab24
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/test_DASTool.log
contains:
- "DAS Tool run on"
- path: output/dastool/test_DASTool_scaffolds2bin.txt
- path: output/dastool/test_DASTool_contig2bin.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/test_DASTool_summary.txt
md5sum: a3efa8717b30dfada78dc5ae9a3dc396
- path: output/dastool/test_DASTool_summary.tsv
md5sum: ab9dd3709a59a69bc66030b9e0ff3d5b
- path: output/dastool/test_proteins.faa
- path: output/dastool/test_proteins.faa.all.b6
md5sum: 39c11237ef22ac73109aaac267e185d0
- path: output/dastool/test_proteins.faa.archaea.scg
md5sum: e79d82eecee25821d1658ea4f082601d
- path: output/dastool/test_proteins.faa.bacteria.scg
md5sum: 8132cfb17cf398d41c036ead55c96ffe
- path: output/dastool/test_test.tsv.eval
md5sum: a3efa8717b30dfada78dc5ae9a3dc396
- path: output/metabat2/bins/test.1.fa.gz
md5sum: 2b297bf557cc3831b800348859331268
- path: output/metabat2/test.tsv.gz
md5sum: 619338fa5019e361d5545ce385a6961f
- path: output/metabat2/test.txt.gz
md5sum: 745a0446af6ef68b930975e9ce5a95d6
- path: output/dastool/test_proteins.faa.findSCG.b6
md5sum: 48e90e12cd6c88d00608777dbc48a82a
- path: output/dastool/test_proteins.faa.scg.candidates.faa
md5sum: d94b7bed0f8aa9cf2824d72c548c537c
- path: output/dastool/versions.yml
md5sum: 004e04c6a38652df2e0c59c44e29c9de

View file

@ -0,0 +1,48 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GUNZIP } from '../../../../modules/gunzip/main.nf'
include { METABAT2_METABAT2 } from '../../../../modules/metabat2/metabat2/main.nf'
include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../modules/metabat2/jgisummarizebamcontigdepths/main.nf'
include { DASTOOL_FASTATOCONTIG2BIN } from '../../../../modules/dastool/fastatocontig2bin/main.nf'
workflow test_dastool_fastatocontig2bin {
input_depth = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
.map { it -> [[ id:'test', single_end:false ], it] }
.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
.set { input_metabat2 }
METABAT2_METABAT2 ( input_metabat2 )
DASTOOL_FASTATOCONTIG2BIN ( METABAT2_METABAT2.out.fasta.collect(), "fa")
}
workflow test_dastool_fastatocontig2bin_ungzipped {
input_depth = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['illumina']['test1_paired_end_sorted_bam_bai'], checkIfExists: true) ]
METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input_depth )
Channel.fromPath(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
.map { it -> [[ id:'test', single_end:false ], it] }
.join(METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS.out.depth)
.set { input_metabat2 }
METABAT2_METABAT2 ( input_metabat2 )
// TODO test unzipped input files
ch_input_2_fastatocontig2bin = GUNZIP( METABAT2_METABAT2.out.fasta ).gunzip
DASTOOL_FASTATOCONTIG2BIN ( ch_input_2_fastatocontig2bin, "fa")
}

View file

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

View file

@ -0,0 +1,20 @@
- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin
command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin -c tests/config/nextflow.config
tags:
- dastool
- dastool/fastatocontig2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml
md5sum: ff4b6f14bee4548bf09b5e602c306595
- name: dastool fastatocontig2bin test_dastool_fastatocontig2bin_ungzipped
command: nextflow run tests/modules/dastool/fastatocontig2bin -entry test_dastool_fastatocontig2bin_ungzipped -c tests/config/nextflow.config
tags:
- dastool
- dastool/fastatocontig2bin
files:
- path: output/dastool/test.tsv
md5sum: 6e46c0be14dded7cb13af38f54feea47
- path: output/dastool/versions.yml

View file

@ -0,0 +1,15 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GSTAMA_POLYACLEANUP } from '../../../../modules/gstama/polyacleanup/main.nf'
workflow test_gstama_polyacleanup {
input = [
[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['transcriptome_fasta'], checkIfExists: true)
]
GSTAMA_POLYACLEANUP ( input )
}

View file

@ -0,0 +1,6 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
ext.prefix = { "${meta.id}_tama" }
}

View file

@ -0,0 +1,14 @@
- name: gstama polyacleanup test_gstama_polyacleanup
command: nextflow run tests/modules/gstama/polyacleanup -entry test_gstama_polyacleanup -c tests/config/nextflow.config
tags:
- gstama
- gstama/polyacleanup
files:
- path: output/gstama/test_tama.fa.gz
md5sum: 9c768387478e5f966a42c369c0270b09
- path: output/gstama/test_tama_polya_flnc_report.txt.gz
md5sum: fe3606979ed11538aacd83159f4cff03
- path: output/gstama/test_tama_tails.fa.gz
md5sum: ba21256c0afe0bda71b3ee66b4c761bf
- path: output/gstama/versions.yml
md5sum: 07ebb812ae13a350d955fab7600b2542

View file

@ -7,28 +7,30 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf'
workflow test_manta_germline {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
[],[]
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [[],[]]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}
workflow test_manta_germline_target_bed {
input = [
[ id:'test'], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)],
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}
workflow test_manta_germline_target_bed_jointcalling {
@ -37,12 +39,14 @@ workflow test_manta_germline_target_bed_jointcalling {
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)],
[file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),],
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
bed = [
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true),
]
MANTA_GERMLINE ( input, fasta, fai )
MANTA_GERMLINE ( input, fasta, fai, bed )
}

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

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

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@ -0,0 +1,23 @@
- name: phantompeakqualtools test_phantompeakqualtools_single_end
command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_single_end -c tests/config/nextflow.config
tags:
- phantompeakqualtools
files:
- path: output/phantompeakqualtools/test.spp.Rdata
- path: output/phantompeakqualtools/test.spp.out
md5sum: b01d976506b6fe45b66c821b1e8a1d15
- path: output/phantompeakqualtools/test.spp.pdf
- path: output/phantompeakqualtools/versions.yml
md5sum: 6c2ede1aac4c574e3c72fbe09f15c03f
- name: phantompeakqualtools test_phantompeakqualtools_paired_end
command: nextflow run tests/modules/phantompeakqualtools -entry test_phantompeakqualtools_paired_end -c tests/config/nextflow.config
tags:
- phantompeakqualtools
files:
- path: output/phantompeakqualtools/test.spp.Rdata
- path: output/phantompeakqualtools/test.spp.out
md5sum: eed46e75eab119224f397a7a8b5924e6
- path: output/phantompeakqualtools/test.spp.pdf
- path: output/phantompeakqualtools/versions.yml
md5sum: 383d2dd583fcb40451bde0d3840bdb72

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@ -0,0 +1,24 @@
#!/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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@ -0,0 +1,9 @@
process {
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
withName: PRINSEQPLUSPLUS {
ext.args = "-lc_entropy=0.8"
}
}

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@ -0,0 +1,27 @@
- 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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@ -0,0 +1,58 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SEQKIT_STATS } from '../../../../modules/seqkit/stats/main.nf'
workflow test_seqkit_stats_single_end {
input = [
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
SEQKIT_STATS ( input )
}
workflow test_seqkit_stats_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)
]
]
SEQKIT_STATS ( input )
}
workflow test_seqkit_stats_nanopore {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
]
SEQKIT_STATS ( input )
}
workflow test_seqkit_stats_genome_fasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
]
SEQKIT_STATS ( input )
}
workflow test_seqkit_stats_transcriptome_fasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true),
]
SEQKIT_STATS ( input )
}

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

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@ -0,0 +1,54 @@
- name: seqkit stats test_seqkit_stats_single_end
command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_single_end -c tests/config/nextflow.config
tags:
- seqkit/stats
- seqkit
files:
- path: output/seqkit/test.tsv
md5sum: e23227d089a7e04b0ec0cb547c4aadff
- path: output/seqkit/versions.yml
md5sum: d67f0c16feb9df77b11f6c91bbdf9926
- name: seqkit stats test_seqkit_stats_paired_end
command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_paired_end -c tests/config/nextflow.config
tags:
- seqkit/stats
- seqkit
files:
- path: output/seqkit/test.tsv
md5sum: 9de20dc39fb01285e3f0c382fda9db52
- path: output/seqkit/versions.yml
md5sum: bd8881933b953d07f2600e2e6a88ebf3
- name: seqkit stats test_seqkit_stats_nanopore
command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_nanopore -c tests/config/nextflow.config
tags:
- seqkit/stats
- seqkit
files:
- path: output/seqkit/test.tsv
md5sum: 5da1709eb5ae64fa3b2d624bffe2e7aa
- path: output/seqkit/versions.yml
md5sum: 565632701fbe048f7ba99f1865bd48ca
- name: seqkit stats test_seqkit_stats_genome_fasta
command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_genome_fasta -c tests/config/nextflow.config
tags:
- seqkit/stats
- seqkit
files:
- path: output/seqkit/test.tsv
md5sum: f64489767a4e769539ef3faf83260184
- path: output/seqkit/versions.yml
md5sum: 782fcdeaa922c8bb532ffa5808849d87
- name: seqkit stats test_seqkit_stats_transcriptome_fasta
command: nextflow run tests/modules/seqkit/stats -entry test_seqkit_stats_transcriptome_fasta -c tests/config/nextflow.config
tags:
- seqkit/stats
- seqkit
files:
- path: output/seqkit/test.tsv
md5sum: fbb975b665a08c8862fcd1268613a945
- path: output/seqkit/versions.yml
md5sum: db99b016d986d26102ec398264a58410

View file

@ -0,0 +1,24 @@
#!/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 )
}

View file

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

View file

@ -0,0 +1,27 @@
- 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