mirror of
https://github.com/MillironX/nf-core_modules.git
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Merge branch 'master' into motus_profile
This commit is contained in:
commit
671bacb6df
60 changed files with 617 additions and 159 deletions
68
modules/antismash/antismashlite/main.nf
Normal file
68
modules/antismash/antismashlite/main.nf
Normal file
|
@ -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
|
||||
"""
|
||||
}
|
128
modules/antismash/antismashlite/meta.yml
Normal file
128
modules/antismash/antismashlite/meta.yml
Normal file
|
@ -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"
|
|
@ -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 ${prefix}.unmapped_1.fastq.gz
|
||||
|
|
|
@ -29,6 +29,15 @@ input:
|
|||
type: file
|
||||
description: Bowtie2 genome index files
|
||||
pattern: "*.ebwt"
|
||||
- save_unaligned:
|
||||
type: boolean
|
||||
description: |
|
||||
Save reads that do not map to the reference (true) or discard them (false)
|
||||
(default: false)
|
||||
- sort_bam:
|
||||
type: boolean
|
||||
description: use samtools sort (true) or samtools view (false)
|
||||
pattern: "true or false"
|
||||
output:
|
||||
- bam:
|
||||
type: file
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYBQSR_SPARK {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.3.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_APPLYVQSR {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR_SPARK {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.3.0--hdfd78af_0' :
|
||||
'broadinstitute/gatk:4.2.3.0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bed)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(pileup), path(matched)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_COMBINEGVCFS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_idx)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
path fasta
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(genomicsdb)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(reads)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(orientationbias), path(segmentation), path(table), val(estimate)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(table)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GATHERPILEUPSUMMARIES {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
|
||||
input:
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GENOTYPEGVCFS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_GETPILEUPSUMMARIES {
|
|||
tag "$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 . \\
|
||||
$args
|
||||
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(feature_file)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOBED {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(f1r2)
|
||||
|
|
|
@ -1,11 +1,11 @@
|
|||
process GATK4_MARKDUPLICATES {
|
||||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(aligned), path(unmapped)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEMUTECTSTATS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(stats)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MERGEVCFS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_MUTECT2 {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(input), path(input_index), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_REVERTSAM {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SELECTVARIANTS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(vcf_idx)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(bam), path(bai), path(intervals)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
|
@ -2,10 +2,10 @@ process GATK4_VARIANTRECALIBRATOR {
|
|||
tag "$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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
|
||||
'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }"
|
||||
'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
|
||||
'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
|
||||
|
||||
input:
|
||||
tuple val(meta), path(vcf), path(tbi)
|
||||
|
|
37
modules/maxquant/lfq/main.nf
Normal file
37
modules/maxquant/lfq/main.nf
Normal file
|
@ -0,0 +1,37 @@
|
|||
process MAXQUANT_LFQ {
|
||||
tag "$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 .
|
||||
"""
|
||||
}
|
52
modules/maxquant/lfq/meta.yml
Normal file
52
modules/maxquant/lfq/meta.yml
Normal 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"
|
|
@ -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/**
|
||||
|
|
|
@ -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"
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
46
tests/modules/antismash/antismashlite/main.nf
Normal file
46
tests/modules/antismash/antismashlite/main.nf
Normal 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] } )
|
||||
}
|
5
tests/modules/antismash/antismashlite/nextflow.config
Normal file
5
tests/modules/antismash/antismashlite/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
35
tests/modules/antismash/antismashlite/test.yml
Normal file
35
tests/modules/antismash/antismashlite/test.yml
Normal 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
|
|
@ -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 )
|
||||
}
|
||||
|
|
|
@ -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:
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -1,6 +1,5 @@
|
|||
process {
|
||||
|
||||
ext.args = "--tmp-dir ."
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
@ -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 )
|
||||
|
|
|
@ -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 {
|
||||
|
||||
|
|
|
@ -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:
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
|
@ -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
|
||||
|
|
17
tests/modules/maxquant/lfq/main.nf
Normal file
17
tests/modules/maxquant/lfq/main.nf
Normal 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() )
|
||||
}
|
5
tests/modules/maxquant/lfq/nextflow.config
Normal file
5
tests/modules/maxquant/lfq/nextflow.config
Normal file
|
@ -0,0 +1,5 @@
|
|||
process {
|
||||
|
||||
publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
|
||||
|
||||
}
|
8
tests/modules/maxquant/lfq/test.yml
Normal file
8
tests/modules/maxquant/lfq/test.yml
Normal 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
|
Loading…
Reference in a new issue