Merge branch 'master' into motus_profile

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JIANHONG OU 2022-05-16 17:34:49 -04:00 committed by GitHub
commit 671bacb6df
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60 changed files with 617 additions and 159 deletions

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@ -0,0 +1,68 @@
process ANTISMASH_ANTISMASHLITE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/antismash-lite:6.0.1--pyhdfd78af_1' :
'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
containerOptions {
workflow.containerEngine == 'singularity' ?
"-B $antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
workflow.containerEngine == 'docker' ?
"-v \$PWD/$antismash_dir:/usr/local/lib/python3.8/site-packages/antismash" :
''
}
input:
tuple val(meta), path(sequence_input)
path(databases)
path(antismash_dir) // Optional input: AntiSMASH installation folder. It is not needed for using this module with conda, but required for docker/singularity (see meta.yml).
path(gff)
output:
tuple val(meta), path("${prefix}/clusterblast/*_c*.txt") , optional: true, emit: clusterblast_file
tuple val(meta), path("${prefix}/{css,images,js}") , emit: html_accessory_files
tuple val(meta), path("${prefix}/knownclusterblast/region*/ctg*.html") , optional: true, emit: knownclusterblast_html
tuple val(meta), path("${prefix}/knownclusterblast/*_c*.txt") , optional: true, emit: knownclusterblast_txt
tuple val(meta), path("${prefix}/svg/clusterblast*.svg") , optional: true, emit: svg_files_clusterblast
tuple val(meta), path("${prefix}/svg/knownclusterblast*.svg") , optional: true, emit: svg_files_knownclusterblast
tuple val(meta), path("${prefix}/*.gbk") , emit: gbk_input
tuple val(meta), path("${prefix}/*.json") , emit: json_results
tuple val(meta), path("${prefix}/*.log") , emit: log
tuple val(meta), path("${prefix}/*.zip") , emit: zip
tuple val(meta), path("${prefix}/*region*.gbk") , emit: gbk_results
tuple val(meta), path("${prefix}/clusterblastoutput.txt") , optional: true, emit: clusterblastoutput
tuple val(meta), path("${prefix}/index.html") , emit: html
tuple val(meta), path("${prefix}/knownclusterblastoutput.txt") , optional: true, emit: knownclusterblastoutput
tuple val(meta), path("${prefix}/regions.js") , emit: json_sideloading
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
gff_flag = "--genefinding-gff3 ${gff}"
"""
## We specifically do not include annotations (--genefinding-tool none) as
## this should be run as a separate module for versioning purposes
antismash \\
$args \\
$gff_flag \\
-c $task.cpus \\
--output-dir $prefix \\
--genefinding-tool none \\
--logfile $prefix/${prefix}.log \\
--databases $databases \\
$sequence_input
cat <<-END_VERSIONS > versions.yml
"${task.process}":
antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
END_VERSIONS
"""
}

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@ -0,0 +1,128 @@
name: antismash_antismashlite
description: |
antiSMASH allows the rapid genome-wide identification, annotation
and analysis of secondary metabolite biosynthesis gene clusters.
keywords:
- secondary metabolites
- BGC
- biosynthetic gene cluster
- genome mining
- NRPS
- RiPP
- antibiotics
- prokaryotes
- bacteria
- eukaryotes
- fungi
- antismash
tools:
- antismashlite:
description: "antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell"
homepage: "https://docs.antismash.secondarymetabolites.org"
documentation: "https://docs.antismash.secondarymetabolites.org"
tool_dev_url: "https://github.com/antismash/antismash"
doi: "10.1093/nar/gkab335"
licence: "['AGPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- sequence_input:
type: file
description: nucleotide sequence file (annotated)
pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
- databases:
type: directory
description: downloaded AntiSMASH databases e.g. data/databases
pattern: "*/"
- antismash_dir:
type: directory
description: |
A local copy of an AntiSMASH installation folder. This is required when running with
docker and singularity (not required for conda), due to attempted 'modifications' of
files during database checks in the installation directory, something that cannot
be done in immutable docker/singularity containers. Therefore, a local installation
directory needs to be mounted (including all modified files from the downloading step)
to the container as a workaround.
pattern: "*/"
- gff:
type: file
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"
- clusterblast_file:
type: file
description: Output of ClusterBlast algorithm
pattern: "clusterblast/*_c*.txt"
- html_accessory_files:
type: directory
description: Accessory files for the HTML output
pattern: "{css/,images/,js/}"
- knownclusterblast_html:
type: file
description: Tables with MIBiG hits in HTML format
pattern: "knownclusterblast/region*/ctg*.html"
- knownclusterblast_txt:
type: file
description: Tables with MIBiG hits
pattern: "knownclusterblast/*_c*.txt"
- svg_files_clusterblast:
type: file
description: SVG images showing the % identity of the aligned hits against their queries
pattern: "svg/clusterblast*.svg"
- svg_files_knownclusterblast:
type: file
description: SVG images showing the % identity of the aligned hits against their queries
pattern: "svg/knownclusterblast*.svg"
- gbk_input:
type: file
description: Nucleotide sequence and annotations in GenBank format; converted from input file
pattern: "*.gbk"
- json_results:
type: file
description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input)
pattern: "*.json"
- log:
type: file
description: Contains all the logging output that antiSMASH produced during its run
pattern: "*.log"
- zip:
type: file
description: Contains a compressed version of the output folder in zip format
pattern: "*.zip"
- gbk_results:
type: file
description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit
pattern: "*region*.gbk"
- clusterblastoutput:
type: file
description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm
pattern: "clusterblastoutput.txt"
- html:
type: file
description: Graphical web view of results in HTML format
patterN: "index.html"
- knownclusterblastoutput:
type: file
description: Raw BLAST output of known clusters of the MIBiG database
pattern: "knownclusterblastoutput.txt"
- json_sideloading:
type: file
description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading")
pattern: "regions.js"
authors:
- "@jasmezz"

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@ -11,6 +11,7 @@ process BOWTIE2_ALIGN {
tuple val(meta), path(reads)
path index
val save_unaligned
val sort_bam
output:
tuple val(meta), path("*.bam") , emit: bam
@ -36,8 +37,7 @@ process BOWTIE2_ALIGN {
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
}
def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
def samtools_command = sort_bam ? 'sort' : 'view'
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
@ -51,7 +51,7 @@ process BOWTIE2_ALIGN {
$unaligned \\
$args \\
2> ${prefix}.bowtie2.log \\
| $samtools_command
| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz

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@ -29,6 +29,15 @@ input:
type: file
description: Bowtie2 genome index files
pattern: "*.ebwt"
- save_unaligned:
type: boolean
description: |
Save reads that do not map to the reference (true) or discard them (false)
(default: false)
- sort_bam:
type: boolean
description: use samtools sort (true) or samtools view (false)
pattern: "true or false"
output:
- bam:
type: file

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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

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@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)

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@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)

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@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)

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@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.3.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
'broadinstitute/gatk:4.2.3.0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)

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@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bed)

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@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(pileup), path(matched)

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@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_idx)

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@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
tag "$fasta"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
path fasta

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@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(genomicsdb)

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@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input)

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@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(reads)

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@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)

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@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(table)

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@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:

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@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)

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@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
tag "$meta.id"
label 'process_high'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)

View file

@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(index), path(intervals)
@ -40,7 +40,7 @@ process GATK4_GETPILEUPSUMMARIES {
--variant $variants \\
--output ${prefix}.pileups.table \\
$reference_command \\
$sites_command \\
$interval_command \\
--tmp-dir . \\
$args

View file

@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)

View file

@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(feature_file)

View file

@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(intervals)

View file

@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(intervals)

View file

@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(f1r2)

View file

@ -1,11 +1,11 @@
process GATK4_MARKDUPLICATES {
tag "$meta.id"
label 'process_low'
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

View file

@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(aligned), path(unmapped)

View file

@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(stats)

View file

@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf)

View file

@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(input), path(input_index), path(intervals)

View file

@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

View file

@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam)

View file

@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(vcf_idx)

View file

@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(bam), path(bai), path(intervals)

View file

@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi)

View file

@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
input:
tuple val(meta), path(vcf), path(tbi)

View file

@ -0,0 +1,37 @@
process MAXQUANT_LFQ {
tag "$meta.id"
label 'process_long'
conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1"
} else {
container "quay.io/biocontainers/maxquant:2.0.3.0--py310hdfd78af_1"
}
input:
tuple val(meta), path(fasta), path(paramfile)
path raw
output:
tuple val(meta), path("*.txt"), emit: maxquant_txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cat <<-END_VERSIONS > versions.yml
"${task.process}":
maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \")
END_VERSIONS
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
mkdir temp
maxquant mqpar_changed.xml
mv combined/txt/*.txt .
"""
}

View file

@ -0,0 +1,52 @@
name: maxquant_lfq
description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER"
keywords:
- sort
tools:
- maxquant:
description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted.
homepage: None
documentation: None
tool_dev_url: None
doi: ""
licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- raw:
type: file
description: raw files with mass spectra
pattern: "*.{raw,RAW,Raw}"
- fasta:
type: file
description: fasta file with protein sequences
pattern: "*.{fasta}"
- parfile:
type: file
description: MaxQuant parameter file (XML)
pattern: "*.{xml}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software version
pattern: "versions.yml"
- maxquant_txt:
type: file
description: tables with peptides and protein information
pattern: "*.{txt}"
authors:
- "@veitveit"

View file

@ -42,6 +42,10 @@ amrfinderplus/update:
- modules/amrfinderplus/update/**
- tests/modules/amrfinderplus/update/**
antismash/antismashlite:
- modules/antismash/antismashlite/**
- tests/modules/antismash/antismashlite/**
antismash/antismashlitedownloaddatabases:
- modules/antismash/antismashlitedownloaddatabases/**
- tests/modules/antismash/antismashlitedownloaddatabases/**
@ -1206,6 +1210,10 @@ maxbin2:
- modules/maxbin2/**
- tests/modules/maxbin2/**
maxquant/lfq:
- modules/maxquant/lfq/**
- tests/modules/maxquant/lfq/**
md5sum:
- modules/md5sum/**
- tests/modules/md5sum/**

View file

@ -430,5 +430,17 @@ params {
ncbi_user_settings = "${test_data_dir}/generic/config/ncbi_user_settings.mkfg"
}
}
'proteomics' {
'msspectra' {
ups_file1 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_12.raw"
ups_file2 = "${test_data_dir}/proteomics/msspectra/OVEMB150205_14.raw"
}
'database' {
yeast_ups = "${test_data_dir}/proteomics/database/yeast_UPS.fasta"
}
'parameter' {
maxquant = "${test_data_dir}/proteomics/parameter/mqpar.xml"
}
}
}
}

View file

@ -0,0 +1,46 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ANTISMASH_ANTISMASHLITE } from '../../../../modules/antismash/antismashlite/main.nf'
include { ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES } from '../../../modules/antismash/antismashlitedownloaddatabases/main.nf'
include { GUNZIP as GUNZIP1 } from '../../../../modules/gunzip/main.nf'
include { GUNZIP as GUNZIP2 } from '../../../../modules/gunzip/main.nf'
include { UNTAR as UNTAR1 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR2 } from '../../../../modules/untar/main.nf'
include { UNTAR as UNTAR3 } from '../../../../modules/untar/main.nf'
workflow test_antismashlite {
genome_fna = [
[ id:'test' ],
file(params.test_data['bacteroides_fragilis']['genome']['genome_fna_gz'], checkIfExists: true)
]
genome_gff = [
[],
file(params.test_data['bacteroides_fragilis']['genome']['genome_gff_gz'], checkIfExists: true)
]
antismash_css = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/css.tar.gz', checkIfExists: true)
]
antismash_detection = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/detection.tar.gz', checkIfExists: true)
]
antismash_modules = [
[],
file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/antismash/modules.tar.gz', checkIfExists: true)
]
GUNZIP1 ( genome_fna )
GUNZIP2 ( genome_gff )
UNTAR1 ( antismash_css )
UNTAR2 ( antismash_detection )
UNTAR3 ( antismash_modules )
ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES ( UNTAR1.out.untar.map{ it[1] }, UNTAR2.out.untar.map{ it[1] }, UNTAR3.out.untar.map{ it[1] } )
ANTISMASH_ANTISMASHLITE ( GUNZIP1.out.gunzip, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.database, ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES.out.antismash_dir, GUNZIP2.out.gunzip.map{ it[1] } )
}

View file

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

View file

@ -0,0 +1,35 @@
- name: antismash antismashlite test_antismashlite
command: nextflow run tests/modules/antismash/antismashlite -entry test_antismashlite -c tests/config/nextflow.config
tags:
- antismash/antismashlite
- antismash
files:
- path: output/antismash/test/NZ_CP069563.1.region001.gbk
contains: ['/tool="antismash"']
- path: output/antismash/test/NZ_CP069563.1.region002.gbk
contains: ['/tool="antismash"']
- path: output/antismash/test/css/bacteria.css
md5sum: 8b3c2f8b143d5245a5f42f55803c532c
- path: output/antismash/test/genome.gbk
contains: ['/tool="antismash"']
- path: output/antismash/test/genome.json
contains: ['{"version": "6.0.1", "input_file": "genome.fna", "records": [{"id": "NZ_CP069563.1", "seq": {"data":']
- path: output/antismash/test/genome.zip
- path: output/antismash/test/index.html
md5sum: de787e865c3a1eec143a19d2facb4de4
- path: output/antismash/test/js/antismash.js
md5sum: 58e90c3d783ae014cc3d51849bcb50a2
- path: output/antismash/test/js/jquery.js
md5sum: 397754ba49e9e0cf4e7c190da78dda05
- path: output/antismash/test/js/jquery.tablesorter.min.js
md5sum: 5e9e08cef4d1be0eaa538e6eb28809a7
- path: output/antismash/test/regions.js
contains: ['"seq_id": "NZ_CP069563.1"']
- path: output/antismash/test/test.log
contains: ["antiSMASH version: 6.0.1"]
- path: output/antismash/versions.yml
md5sum: 759431a43da33e2ef8e2d0ebd79a439b
- path: output/gunzip1/genome.fna
md5sum: dafd38f5454b54fbea38245d773062a5
- path: output/gunzip2/genome.gff
md5sum: 9b9c848b1946d43fa68128f4d6316052

View file

@ -14,9 +14,25 @@ workflow test_bowtie2_align_single_end {
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
sort = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}
workflow test_bowtie2_align_single_end_sorted {
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)
save_unaligned = false
sort = true
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}
workflow test_bowtie2_align_paired_end {
@ -29,9 +45,26 @@ workflow test_bowtie2_align_paired_end {
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
sort = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}
workflow test_bowtie2_align_paired_end_sorted {
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)
save_unaligned = false
sort = true
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}
workflow test_bowtie2_align_single_end_large_index {
@ -43,9 +76,10 @@ workflow test_bowtie2_align_single_end_large_index {
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
sort = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}
workflow test_bowtie2_align_paired_end_large_index {
@ -58,7 +92,8 @@ workflow test_bowtie2_align_paired_end_large_index {
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
save_unaligned = false
sort = false
BOWTIE2_BUILD ( fasta )
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned )
}
BOWTIE2_ALIGN ( input, BOWTIE2_BUILD.out.index, save_unaligned, sort )
}

View file

@ -8,6 +8,16 @@
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/versions.yml
- name: bowtie2 align test_bowtie2_align_single_end_sorted
command: nextflow run ./tests/modules/bowtie2/align -entry test_bowtie2_align_single_end_sorted -c ./tests/config/nextflow.config -c ./tests/modules/bowtie2/align/nextflow.config
tags:
- bowtie2
- bowtie2/align
files:
- path: ./output/bowtie2/test.bam
- path: ./output/bowtie2/test.bowtie2.log
- path: ./output/bowtie2/versions.yml
- name: bowtie2 align test_bowtie2_align_paired_end
command: nextflow run tests/modules/bowtie2/align -entry test_bowtie2_align_paired_end -c tests/config/nextflow.config -c tests/modules/bowtie2/align/nextflow.config
tags:

View file

@ -5,7 +5,7 @@
- gatk4/applybqsr
files:
- path: output/gatk4/test.bam
md5sum: d088422be886dc8507ff97fcc7dd968a
md5sum: e11b7eaf2034740a953626518e3c3d6e
- path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_intervals
@ -15,7 +15,7 @@
- gatk4/applybqsr
files:
- path: output/gatk4/test.bam
md5sum: 4bfa18d651abd945e240b05e70107716
md5sum: e9e9aa753c106e43f936ad573e23d2e6
- path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_cram
@ -25,5 +25,5 @@
- gatk4/applybqsr
files:
- path: output/gatk4/test.cram
md5sum: 2e0bca197af4f043a4a85152e6edbe04
md5sum: bca9d234a5d484ce2a6f4826ca2ea308
- path: output/gatk4/versions.yml

View file

@ -5,7 +5,7 @@
- gatk4/applybqsrspark
files:
- path: output/gatk4/test.bam
md5sum: d088422be886dc8507ff97fcc7dd968a
md5sum: 1901c819fcba0fdd5e2482e6dc8285ef
- path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_intervals
@ -15,7 +15,7 @@
- gatk4/applybqsrspark
files:
- path: output/gatk4/test.bam
md5sum: 4bfa18d651abd945e240b05e70107716
md5sum: 2ca2446f0125890280056fd7da822732
- path: output/gatk4/versions.yml
- name: gatk4 applybqsr test_gatk4_applybqsr_spark_cram
@ -25,5 +25,5 @@
- gatk4/applybqsrspark
files:
- path: output/gatk4/test.cram
md5sum: 2e0bca197af4f043a4a85152e6edbe04
md5sum: 60f7c822a9f2833e11eb7bfd16e4421f
- path: output/gatk4/versions.yml

View file

@ -1,6 +1,5 @@
process {
ext.args = "--tmp-dir ."
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
}
}

View file

@ -65,7 +65,9 @@ workflow test_gatk4_genotypegvcfs_gz_input_intervals {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
file(params.test_data['homo_sapiens']['genome']['genome_bed'], 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)
@ -80,7 +82,8 @@ workflow test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true),
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true),
[]
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
@ -106,6 +109,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input {
gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([])
gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
@ -128,6 +132,7 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp {
gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([])
gendb.add([])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi)
@ -146,6 +151,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_intervals {
gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, [], [] )
@ -167,6 +174,8 @@ workflow test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals {
gendb = UNTAR.out.untar.map{ it[1] }.collect()
gendb.add([])
gendb.add([file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)])
gendb.add([])
input = Channel.of([ id:'test' ]).combine(gendb)
GATK4_GENOTYPEGVCFS ( input, fasta, fai, dict, dbsnp, dbsnp_tbi )

View file

@ -4,21 +4,6 @@ nextflow.enable.dsl = 2
include { GATK4_GETPILEUPSUMMARIES } from '../../../../modules/gatk4/getpileupsummaries/main.nf'
workflow test_gatk4_getpileupsummaries_just_variants {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) ,
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true),
[]
]
variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true)
variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true)
fasta = []
fai = []
dict = []
GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi )
}
workflow test_gatk4_getpileupsummaries_separate_sites {

View file

@ -1,13 +1,3 @@
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config
tags:
- gatk4/getpileupsummaries
- gatk4
files:
- path: output/gatk4/test.pileups.table
md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469
- path: output/gatk4/versions.yml
- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites
command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config
tags:

View file

@ -7,11 +7,11 @@
- path: output/gatk4/test.interval_list
md5sum: e51101c9357fb2d59fd30e370eefa39c
- path: output/gatk4/test_split/temp_0001_of_6/1scattered.interval_list
md5sum: b8ba8a387200df76a0d1c577626dc265
md5sum: 39385d38ac6cb7c05190026fc3b81411
- path: output/gatk4/test_split/temp_0002_of_6/2scattered.interval_list
md5sum: 0728d164666d9264ef442a493e008dee
md5sum: 59f1978c5f4ef3fce3b110816283d9f5
- path: output/gatk4/test_split/temp_0003_of_6/3scattered.interval_list
md5sum: 55da0f3c69504148f4e7002a0e072cfe
md5sum: 709fe81bfcf700bd80d96c62a71629fd
- path: output/gatk4/test_split/temp_0004_of_6/4scattered.interval_list
md5sum: d29ca4447f32547f2936567fa902796a
md5sum: c24044490cfedbcba61dbc646d3aa570
- path: output/gatk4/versions.yml

View file

@ -5,9 +5,9 @@
- gatk4/markduplicates
files:
- path: output/gatk4/test.bai
md5sum: e9c125e82553209933883b4fe2b8d7c2
md5sum: c8f7a9e426c768577f88f59cb1336bf3
- path: output/gatk4/test.bam
md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9
md5sum: 58533ddab47f7ac07f7b10e7f4aac234
- path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml
@ -20,6 +20,6 @@
- path: output/gatk4/test.bai
md5sum: bad71df9c876e72a5bc0a3e0fd755f92
- path: output/gatk4/test.bam
md5sum: 8187febc6108ffef7f907e89b9c091a4
md5sum: 112580c24b43331950f24f9adea30788
- path: output/gatk4/test.metrics
- path: output/gatk4/versions.yml

View file

@ -5,7 +5,7 @@
- gatk4/splitncigarreads
files:
- path: output/gatk4/test.bam
md5sum: 436d8e31285c6b588bdd1c7f1d07f6f2
md5sum: 37e5dbce8692b54c3292b539c91dfbd7
- path: output/gatk4/versions.yml
- name: gatk4 splitncigarreads test_gatk4_splitncigarreads_intervals
command: nextflow run tests/modules/gatk4/splitncigarreads -entry test_gatk4_splitncigarreads_intervals -c tests/config/nextflow.config
@ -14,5 +14,5 @@
- gatk4/splitncigarreads
files:
- path: output/gatk4/test.bam
md5sum: cd56e3225950f519fd47164cca60a0bb
md5sum: e5cd2fd1822298a9bf7bc8b8d42146af
- path: output/gatk4/versions.yml

View file

@ -9,7 +9,7 @@
- "#CHROM POS ID REF ALT QUAL FILTER INFO"
- path: output/gatk4/test.recal.idx
- path: output/gatk4/test.tranches
md5sum: d238e97bf996863969dac7751e345549
md5sum: c029e52fd63a893e1154cc9144a19eeb
- path: output/gatk4/versions.yml
- name: gatk4 variantrecalibrator test_gatk4_variantrecalibrator_allele_specific
@ -23,5 +23,5 @@
- "#CHROM POS ID REF ALT QUAL FILTER INFO"
- path: output/gatk4/test.recal.idx
- path: output/gatk4/test.tranches
md5sum: 444438d46716593634a6817958099292
md5sum: ad52fa69325c758f458a30ee5b43d6b5
- path: output/gatk4/versions.yml

View file

@ -0,0 +1,17 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { MAXQUANT_LFQ } from '../../../../modules/maxquant/lfq/main.nf' addParams( options: [:] )
workflow test_maxquant_lfq {
input = [ [ id:'test' ], // meta map
file(params.test_data['proteomics']['database']['yeast_ups'], checkIfExists: true), file(params.test_data['proteomics']['parameter']['maxquant'] , checkIfExists: true)
]
rawfiles = [file(params.test_data['proteomics']['msspectra']['ups_file1']) , file(params.test_data['proteomics']['msspectra']['ups_file2'])]
MAXQUANT_LFQ ( input, rawfiles.collect() )
}

View file

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

View file

@ -0,0 +1,8 @@
- name: maxquant lfq
command: nextflow run ./tests/modules/maxquant/lfq -entry test_maxquant_lfq -c tests/config/nextflow.config
tags:
- maxquant
- maxquant/lfq
files:
- path: output/maxquant/proteinGroups.txt
md5sum: 0d0f6aab54fe6dc717d1307bbc207324