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Set process label to process_single for modules with no task.cpus usage (#2076)

Browse source 
* Set process label to `process_single` for modules with no `task.cpus` usage

* Fix tests of 'borked' modules

* prettier

* More modules are single-threaded and can use process_single

* Adding process_single to hmmer/esl* modules

* Fix failing tests

* Prettier

Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
This commit is contained in:
James A. Fellows Yates 2022-09-19 11:54:47 +02:00 committed by GitHub
parent 46ad627a73
commit 90aef30f43
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
87 changed files with 157 additions and 192 deletions
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2
modules/abricate/summary/main.nf
View file

@ -1,6 +1,6 @@
process ABRICATE_SUMMARY {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::abricate=1.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/adapterremovalfixprefix/main.nf
View file

@ -1,6 +1,6 @@
process ADAPTERREMOVALFIXPREFIX {
tag "$meta.id"
label 'process_medium'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)

2
modules/ampir/main.nf
View file

@ -1,6 +1,6 @@
process AMPIR {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "conda-forge::r-ampir=1.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/amplify/predict/main.nf
View file

@ -1,6 +1,6 @@
process AMPLIFY_PREDICT {
tag "$meta.id"
label 'process_low'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)

2
modules/amrfinderplus/update/main.nf
View file

@ -1,6 +1,6 @@
process AMRFINDERPLUS_UPDATE {
tag "update"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/antismash/antismashlitedownloaddatabases/main.nf
View file

@ -1,5 +1,5 @@
process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::antismash-lite=6.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bamutil/trimbam/main.nf
View file

@ -1,6 +1,6 @@
process BAMUTIL_TRIMBAM {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::bamutil=1.0.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/bamtobed/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_BAMTOBED {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/complement/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_COMPLEMENT {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/genomecov/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_GENOMECOV {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/getfasta/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_GETFASTA {
tag "$bed"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/intersect/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_INTERSECT {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/makewindows/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_MAKEWINDOWS {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/maskfasta/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_MASKFASTA {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/merge/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_MERGE {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/slop/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_SLOP {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/sort/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_SORT {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/split/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_SPLIT {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bedtools/subtract/main.nf
View file

@ -1,6 +1,6 @@
process BEDTOOLS_SUBTRACT {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bwa/index/main.nf
View file

@ -1,6 +1,6 @@
process BWA_INDEX {
tag "$fasta"
label 'process_high'
label 'process_single'
conda (params.enable_conda ? "bioconda::bwa=0.7.17" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/bwamem2/index/main.nf
View file

@ -1,6 +1,6 @@
process BWAMEM2_INDEX {
tag "$fasta"
label 'process_high'
label 'process_single'
conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/cat/fastq/main.nf
View file

@ -1,6 +1,6 @@
process CAT_FASTQ {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/centrifuge/kreport/main.nf
View file

@ -1,6 +1,6 @@
process CENTRIFUGE_KREPORT {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/damageprofiler/main.nf
View file

@ -1,6 +1,6 @@
process DAMAGEPROFILER {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/dastool/fastatocontig2bin/main.nf
View file

@ -1,6 +1,6 @@
process DASTOOL_FASTATOCONTIG2BIN {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::das_tool=1.1.4" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/dastool/scaffolds2bin/main.nf
View file

@ -1,6 +1,6 @@
process DASTOOL_SCAFFOLDS2BIN {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::das_tool=1.1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/dedup/main.nf
View file

@ -1,6 +1,6 @@
process DEDUP {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::dedup=0.12.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

5
modules/deeparg/downloaddata/main.nf
View file

@ -1,7 +1,5 @@
def VERSION='1.0.2'
process DEEPARG_DOWNLOADDATA {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -25,6 +23,7 @@ process DEEPARG_DOWNLOADDATA {
script:
def args = task.ext.args ?: ''
def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
deeparg \\
download_data \\

5
modules/deeparg/predict/main.nf
View file

@ -1,8 +1,6 @@
def VERSION="1.0.2"
process DEEPARG_PREDICT {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::deeparg=1.0.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@ -31,6 +29,7 @@ process DEEPARG_PREDICT {
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION='1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
deeparg \\
predict \\

2
modules/deepbgc/download/main.nf
View file

@ -1,5 +1,5 @@
process DEEPBGC_DOWNLOAD {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/deepbgc/pipeline/main.nf
View file

@ -1,6 +1,6 @@
process DEEPBGC_PIPELINE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::deepbgc=0.1.30" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/entrezdirect/esearch/main.nf
View file

@ -1,6 +1,6 @@
process ENTREZDIRECT_ESEARCH {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/entrezdirect/esummary/main.nf
View file

@ -1,6 +1,6 @@
process ENTREZDIRECT_ESUMMARY {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/entrezdirect/xtract/main.nf
View file

@ -1,6 +1,6 @@
process ENTREZDIRECT_XTRACT {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::entrez-direct=16.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/gatk/indelrealigner/main.nf
View file

@ -1,6 +1,6 @@
process GATK_INDELREALIGNER {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/goat/taxonsearch/main.nf
View file

@ -1,6 +1,6 @@
process GOAT_TAXONSEARCH {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::goat=0.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/gunc/downloaddb/main.nf
View file

@ -1,6 +1,6 @@
process GUNC_DOWNLOADDB {
tag '$db_name'
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::gunc=1.0.5" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/gunzip/main.nf
View file

@ -1,6 +1,6 @@
process GUNZIP {
tag "$archive"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hamronization/abricate/main.nf
View file

@ -1,6 +1,6 @@
process HAMRONIZATION_ABRICATE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hamronization/amrfinderplus/main.nf
View file

@ -1,7 +1,7 @@
process HAMRONIZATION_AMRFINDERPLUS {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hamronization/deeparg/main.nf
View file

@ -1,6 +1,6 @@
process HAMRONIZATION_DEEPARG {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hamronization/rgi/main.nf
View file

@ -1,7 +1,7 @@
process HAMRONIZATION_RGI {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hamronization/summarize/main.nf
View file

@ -1,5 +1,5 @@
process HAMRONIZATION_SUMMARIZE {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hamronization=1.0.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hmmer/eslalimask/main.nf
View file

@ -1,6 +1,6 @@
process HMMER_ESLALIMASK {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hmmer/eslreformat/main.nf
View file

@ -1,6 +1,6 @@
process HMMER_ESLREFORMAT {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/hmmer/hmmalign/main.nf
View file

@ -1,6 +1,6 @@
process HMMER_HMMALIGN {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::hmmer=3.3.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/kaiju/kaiju2krona/main.nf
View file

@ -1,6 +1,6 @@
process KAIJU_KAIJU2KRONA {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/kaiju/kaiju2table/main.nf
View file

@ -1,6 +1,6 @@
process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/krakentools/combinekreports/main.nf
View file

@ -1,5 +1,5 @@
process KRAKENTOOLS_COMBINEKREPORTS {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/krakentools/kreport2krona/main.nf
View file

@ -1,6 +1,6 @@
process KRAKENTOOLS_KREPORT2KRONA {
tag "$meta.id"
label 'process_low'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)

2
modules/krona/kronadb/main.nf
View file

@ -1,7 +1,7 @@
def VERSION='2.7.1' // Version information not provided by tool on CLI
process KRONA_KRONADB {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/krona/ktimporttaxonomy/main.nf
View file

@ -1,6 +1,6 @@
process KRONA_KTIMPORTTAXONOMY {
tag "${meta.id}"
label 'process_high'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::krona=2.8" : null)

2
modules/krona/ktimporttext/main.nf
View file

@ -1,6 +1,6 @@
process KRONA_KTIMPORTTEXT {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::krona=2.8.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/krona/ktupdatetaxonomy/main.nf
View file

@ -1,7 +1,7 @@
def VERSION='2.7.1' // Version information not provided by tool on CLI
process KRONA_KTUPDATETAXONOMY {
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::krona=2.7.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/mapdamage2/main.nf
View file

@ -1,6 +1,6 @@
process MAPDAMAGE2 {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::mapdamage2=2.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/md5sum/main.nf
View file

@ -1,6 +1,6 @@
process MD5SUM {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "conda-forge::coreutils=9.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/megan/daa2info/main.nf
View file

@ -1,6 +1,6 @@
process MEGAN_DAA2INFO {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/megan/rma2info/main.nf
View file

@ -1,6 +1,6 @@
process MEGAN_RMA2INFO {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/motus/merge/main.nf
View file

@ -2,7 +2,7 @@ VERSION = '3.0.1'
process MOTUS_MERGE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::motus=3.0.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/mtnucratio/main.nf
View file

@ -1,6 +1,6 @@
process MTNUCRATIO {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::mtnucratio=0.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/multiqc/main.nf
View file

@ -1,5 +1,5 @@
process MULTIQC {
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? 'bioconda::multiqc=1.13' : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/multivcfanalyzer/main.nf
View file

@ -1,6 +1,6 @@
process MULTIVCFANALYZER {
tag '$fasta'
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::multivcfanalyzer=0.85.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/muscle/main.nf
View file

@ -1,6 +1,6 @@
process MUSCLE {
tag "$meta.id"
label 'process_medium'
label 'process_single'
conda (params.enable_conda ? "bioconda::muscle=3.8.1551" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/preseq/ccurve/main.nf
View file

@ -1,6 +1,6 @@
process PRESEQ_CCURVE {
tag "$meta.id"
label 'process_medium'
label 'process_single'
label 'error_ignore'
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)

2
modules/preseq/lcextrap/main.nf
View file

@ -1,6 +1,6 @@
process PRESEQ_LCEXTRAP {
tag "$meta.id"
label 'process_medium'
label 'process_single'
label 'error_ignore'
conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)

2
modules/prodigal/main.nf
View file

@ -1,6 +1,6 @@
process PRODIGAL {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "prodigal=2.6.3 pigz=2.6" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/pydamage/filter/main.nf
View file

@ -1,6 +1,6 @@
process PYDAMAGE_FILTER {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::pydamage=0.70" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/seqtk/mergepe/main.nf
View file

@ -1,6 +1,6 @@
process SEQTK_MERGEPE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/seqtk/rename/main.nf
View file

@ -1,6 +1,6 @@
process SEQTK_RENAME {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/seqtk/sample/main.nf
View file

@ -1,6 +1,6 @@
process SEQTK_SAMPLE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/seqtk/seq/main.nf
View file

@ -1,6 +1,6 @@
process SEQTK_SEQ {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/seqtk/subseq/main.nf
View file

@ -1,6 +1,6 @@
process SEQTK_SUBSEQ {
tag '$sequences'
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/sexdeterrmine/main.nf
View file

@ -1,6 +1,6 @@
process SEXDETERRMINE {
tag "$meta.id"
label 'process_low'
label 'process_single'
conda (params.enable_conda ? "bioconda::sexdeterrmine=1.1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

2
modules/ucsc/bedgraphtobigwig/main.nf
View file

@ -1,6 +1,6 @@
process UCSC_BEDGRAPHTOBIGWIG {
tag "$meta.id"
label 'process_medium'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)

2
modules/ucsc/bedtobigbed/main.nf
View file

@ -1,6 +1,6 @@
process UCSC_BEDTOBIGBED {
tag "$meta.id"
label 'process_medium'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null)

2
modules/ucsc/bigwigaverageoverbed/main.nf
View file

@ -1,6 +1,6 @@
process UCSC_BIGWIGAVERAGEOVERBED {
tag "$meta.id"
label 'process_medium'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null)

2
modules/ucsc/wigtobigwig/main.nf
View file

@ -1,6 +1,6 @@
process UCSC_WIGTOBIGWIG {
tag "$meta.id"
label 'process_medium'
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)

2
tests/modules/adapterremovalfixprefix/test.yml
View file

@ -5,5 +5,3 @@
files:
- path: output/adapterremovalfixprefix/test.fq.gz
md5sum: ff956de3532599a56c3efe5369f0953f
- path: output/adapterremovalfixprefix/versions.yml
md5sum: 983cb58079bf015c1d489a7e48261746

123
tests/modules/damageprofiler/test.yml
View file

@ -1,110 +1,77 @@
- name: damageprofiler
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
- name: damageprofiler test_damageprofiler
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
- path: output/damageprofiler/test/3pGtoA_freq.txt
md5sum: 61c903b1504ed7d7182570dfc75e4498
md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
- path: output/damageprofiler/test/5pCtoT_freq.txt
md5sum: 15a75b60ee519b61ce04a83fe3afe855
md5sum: 38b5d7c87ec2d8422bc5587095711c5f
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
md5sum: 05e041ff47e7c6d08ede51f5c81a2464
- path: output/damageprofiler/test/DNA_comp_genome.txt
md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
- path: output/damageprofiler/test/DNA_composition_sample.txt
md5sum: 16be9c91a06fa7defee376230b12862f
- path: output/damageprofiler/test/DamagePlot.pdf
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/dmgprof.json
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
- path: output/damageprofiler/test/DNA_comp_genome.txt
md5sum: fea48af1ecf491b439d36d4a919473df
- path: output/damageprofiler/test/DNA_composition_sample.txt
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/editDistance.txt
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/Length_plot_combined_data.svg
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/dmgprof.json
md5sum: a011a47edaadb3a07527c329a6492570
- path: output/damageprofiler/test/editDistance.txt
md5sum: 7590dac007633ee11025cc99ec9f009b
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/lgdistribution.txt
md5sum: df2e19195185ea9ee05e8e84b2948f36
md5sum: 583fd98094de3fb462b133daeaadcf52
- path: output/damageprofiler/test/misincorporation.txt
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
- name: damageprofiler_reference
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
- name: damageprofiler test_damageprofiler_reference
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_reference -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
- path: output/damageprofiler/test/3pGtoA_freq.txt
md5sum: 61c903b1504ed7d7182570dfc75e4498
md5sum: 56c165bbc9197e0b3d5bd3d464f9e235
- path: output/damageprofiler/test/3p_freq_misincorporations.txt
md5sum: 62e60259dd7fa2b54cdab6afc1adc9c4
- path: output/damageprofiler/test/5pCtoT_freq.txt
md5sum: 15a75b60ee519b61ce04a83fe3afe855
md5sum: 38b5d7c87ec2d8422bc5587095711c5f
- path: output/damageprofiler/test/5p_freq_misincorporations.txt
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
md5sum: 05e041ff47e7c6d08ede51f5c81a2464
- path: output/damageprofiler/test/DNA_comp_genome.txt
md5sum: e4d949c6aceddc2c2ef14de9c4aafde5
- path: output/damageprofiler/test/DNA_composition_sample.txt
md5sum: 16be9c91a06fa7defee376230b12862f
- path: output/damageprofiler/test/DamagePlot.pdf
- path: output/damageprofiler/test/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/dmgprof.json
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
- path: output/damageprofiler/test/DNA_comp_genome.txt
md5sum: fea48af1ecf491b439d36d4a919473df
- path: output/damageprofiler/test/DNA_composition_sample.txt
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/editDistance.txt
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/Length_plot_combined_data.svg
- path: output/damageprofiler/test/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/Length_plot.pdf
- path: output/damageprofiler/test/dmgprof.json
md5sum: a011a47edaadb3a07527c329a6492570
- path: output/damageprofiler/test/editDistance.txt
md5sum: 7590dac007633ee11025cc99ec9f009b
- path: output/damageprofiler/test/edit_distance.pdf
- path: output/damageprofiler/test/edit_distance.svg
- path: output/damageprofiler/test/lgdistribution.txt
md5sum: df2e19195185ea9ee05e8e84b2948f36
md5sum: 583fd98094de3fb462b133daeaadcf52
- path: output/damageprofiler/test/misincorporation.txt
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
md5sum: 25119c0fcc8839fdbb3ed10922fb07f4
- name: damageprofiler_specieslist
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -dump-channels -c ./tests/modules/damageprofiler/nextflow.config
- name: damageprofiler test_damageprofiler_specieslist
command: nextflow run ./tests/modules/damageprofiler -entry test_damageprofiler_specieslist -c ./tests/config/nextflow.config -c ./tests/modules/damageprofiler/nextflow.config
tags:
- damageprofiler
files:
- path: output/damageprofiler/test/chr22/3p_freq_misincorporations.txt
md5sum: de3b84d946a6b63cdcfadf82bf6854c0
- path: output/damageprofiler/test/chr22/3pGtoA_freq.txt
md5sum: 61c903b1504ed7d7182570dfc75e4498
- path: output/damageprofiler/test/chr22/5pCtoT_freq.txt
md5sum: 15a75b60ee519b61ce04a83fe3afe855
- path: output/damageprofiler/test/chr22/5p_freq_misincorporations.txt
md5sum: 3b3240d6c1a3491e461b39199a9fcfe3
- path: output/damageprofiler/test/chr22/DamagePlot_five_prime.svg
- path: output/damageprofiler/test/chr22/DamagePlot.pdf
- path: output/damageprofiler/test/chr22/DamagePlot_three_prime.svg
- path: output/damageprofiler/test/DamageProfiler.log
contains:
- "FINISHED SUCCESSFULLY"
- path: output/damageprofiler/test/chr22/dmgprof.json
md5sum: 2e54e712d2ae9e32c4c298e5fd8f60fe
- path: output/damageprofiler/test/chr22/DNA_comp_genome.txt
md5sum: fea48af1ecf491b439d36d4a919473df
- path: output/damageprofiler/test/chr22/DNA_composition_sample.txt
md5sum: 9e17a0b1e5ad4eb13201cd24ad8507dd
- path: output/damageprofiler/test/chr22/edit_distance.pdf
- path: output/damageprofiler/test/chr22/edit_distance.svg
- path: output/damageprofiler/test/chr22/editDistance.txt
md5sum: 04d14b449a5afa8b5dbff0dfa762356b
- path: output/damageprofiler/test/chr22/Length_plot_combined_data.svg
- path: output/damageprofiler/test/chr22/Length_plot_forward_reverse_separated.svg
- path: output/damageprofiler/test/chr22/Length_plot.pdf
- path: output/damageprofiler/test/chr22/lgdistribution.txt
md5sum: df2e19195185ea9ee05e8e84b2948f36
- path: output/damageprofiler/test/chr22/misincorporation.txt
md5sum: bec0c5fc2fa9c82b04949e2d8b6e979c
#contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'

6
tests/modules/entrezdirect/esummary/test.yml
View file

@ -5,7 +5,7 @@
- entrezdirect/esummary
files:
- path: output/entrezdirect/test_sra.xml
md5sum: bc4bc7f3c53af5961bc8592225959363
contains: ["WGS of ornithorhynchus anatinus"]
- name: entrezdirect esummary test_entrezdirect_esummary_genome
command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config
@ -14,7 +14,7 @@
- entrezdirect/esummary
files:
- path: output/entrezdirect/test_genome.xml
md5sum: af6242f231bdc147d6197edfd0954585
contains: ["Hypsibius dujardini"]
- name: entrezdirect esummary test_entrezdirect_esummary_assembly
command: nextflow run ./tests/modules/entrezdirect/esummary -entry test_entrezdirect_esummary_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/esummary/nextflow.config
@ -23,4 +23,4 @@
- entrezdirect/esummary
files:
- path: output/entrezdirect/test_assembly.xml
md5sum: 32f81147eea61df5814e87c2df1092a9
contains: ["ContigN50"]

12
tests/modules/entrezdirect/xtract/test.yml
View file

@ -1,17 +1,17 @@
- name: entrezdirect xtract test_entrezdirect_xtract_assembly
command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_assembly -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config
tags:
- entrezdirect/xtract
- entrezdirect
- entrezdirect/xtract
files:
- path: output/entrezdirect/test_assembly.xml
md5sum: 32f81147eea61df5814e87c2df1092a9
- path: output/entrezdirect/test_assembly.txt
md5sum: 17073db7c14890aef30f5e3f2d003d32
- name: entrezdirect xtract test_entrezdirect_xtract_genome
command: nextflow run ./tests/modules/entrezdirect/xtract -entry test_entrezdirect_xtract_genome -c ./tests/config/nextflow.config -c ./tests/modules/entrezdirect/xtract/nextflow.config
tags:
- entrezdirect/xtract
- entrezdirect
- entrezdirect/xtract
files:
- path: output/entrezdirect/test_genome.xml
md5sum: af6242f231bdc147d6197edfd0954585
- path: output/entrezdirect/test_genome.txt
md5sum: 931279db7c80c5bb9ed523815898a9cd

4
tests/modules/hamronization/summarize/main.nf
View file

@ -10,12 +10,12 @@ workflow test_hamronization_summarize {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
]
input2 = [
[ id:'test2', single_end:false ], // meta map
file(params.test_data['bacteroides_fragilis']['genome']['genome_mapping_potential_arg'], checkIfExists: true),
file(params.test_data['bacteroides_fragilis']['hamronization']['genome_mapping_potential_arg'], checkIfExists: true),
]
HAMRONIZATION_DEEPARG ( input, 'tsv', '1.0.2', '2' )

6
tests/modules/hamronization/summarize/test.yml
View file

@ -1,8 +1,8 @@
- name: hamronization summarize test_hamronization_summarize
command: nextflow run tests/modules/hamronization/summarize -entry test_hamronization_summarize -c tests/config/nextflow.config
command: nextflow run ./tests/modules/hamronization/summarize -entry test_hamronization_summarize -c ./tests/config/nextflow.config -c ./tests/modules/hamronization/summarize/nextflow.config
tags:
- hamronization
- hamronization/summarize
- hamronization
files:
- path: output/hamronization/hamronization_combined_report.json
md5sum: 1623b6cc3b213208a425e023edd94691
@ -10,5 +10,3 @@
md5sum: 3c315605aca0c5964796bb5fd4cdd522
- path: output/hamronization/test2.tsv
md5sum: 453f38502e35261a50a0849dca34f05b
- path: output/hamronization/versions.yml
md5sum: 99b5046fac643e16ca3362d1baf3284b

8
tests/modules/seqtk/mergepe/test.yml
View file

@ -5,7 +5,9 @@
- seqtk
files:
- path: output/seqtk/test.processed.fastq.gz
md5sum: e325ef7deb4023447a1f074e285761af
contains:
- "@"
- "+"
- name: seqtk mergepe test_seqtk_mergepe_paired_end
command: nextflow run ./tests/modules/seqtk/mergepe -entry test_seqtk_mergepe_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/mergepe/nextflow.config
@ -14,4 +16,6 @@
- seqtk
files:
- path: output/seqtk/test.processed.fastq.gz
md5sum: 3f094ef62d9bfe06aa25174a06bc7d04
contains:
- "@"
- "+"

12
tests/modules/seqtk/rename/test.yml
View file

@ -5,9 +5,8 @@
- seqtk/rename
files:
- path: output/seqtk/test.renamed.fasta.gz
md5sum: 7b407952dcf0d925f1996e04a201d05b
- path: output/seqtk/versions.yml
md5sum: 24127592f1b9e5ee8e5ab04ee748c491
contains:
- ">test1"
- name: seqtk rename test_seqtk_rename_fq
command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config
@ -16,6 +15,7 @@
- seqtk/rename
files:
- path: output/seqtk/test.renamed.fastq.gz
md5sum: babdfc2a3940a1e32a63479db2c1d600
- path: output/seqtk/versions.yml
md5sum: 06c19670eb2b4185e8f4fa5dcf8fb0d5
contains:
- "@test1"
- "@test2"
- "@test3"

9
tests/modules/seqtk/sample/test.yml
View file

@ -5,7 +5,8 @@
- seqtk/sample
files:
- path: output/seqtk/test.sampled.fastq.gz
md5sum: 73c3e8f113860244f3ed3866a8b9d555
contains:
- "@ERR5069949"
- name: seqtk sample test_seqtk_sample_paired_end
command: nextflow run ./tests/modules/seqtk/sample -entry test_seqtk_sample_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/seqtk/sample/nextflow.config
@ -14,6 +15,8 @@
- seqtk/sample
files:
- path: output/seqtk/test.sampled_1.fastq.gz
md5sum: 73c3e8f113860244f3ed3866a8b9d555
contains:
- "@ERR5069949"
- path: output/seqtk/test.sampled_2.fastq.gz
md5sum: 75457ddceea3a5688d05438cdbffba24
contains:
- "@ERR5069949"

7
tests/modules/seqtk/seq/test.yml
View file

@ -6,8 +6,6 @@
files:
- path: output/seqtk/test.seqtk-seq.fasta.gz
md5sum: 50d73992c8c7e56dc095ef47ec52a754
- path: output/seqtk/versions.yml
md5sum: 6555e1061080c44f828de0b40b299e41
- name: seqtk seq test_seqtk_seq_fq
command: nextflow run tests/modules/seqtk/seq -entry test_seqtk_seq_fq -c tests/config/nextflow.config
@ -16,6 +14,5 @@
- seqtk
files:
- path: output/seqtk/test.seqtk-seq.fasta.gz
md5sum: 2f009f1647971a97b4edec726a99dc1a
- path: output/seqtk/versions.yml
md5sum: feb70feb3165d5c19fa50c16e46e6772
contains:
- ">ERR5069949"