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Merge branch 'nf-core:master' into master

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James A. Fellows Yates 2022-03-30 08:56:30 +02:00 committed by GitHub
commit 4b3929371a
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5 changed files with 13 additions and 13 deletions
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6
modules/chromap/chromap/main.nf
View file

@ -2,10 +2,10 @@ process CHROMAP_CHROMAP {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.2.0 bioconda::samtools=1.14" : null)
conda (params.enable_conda ? "bioconda::chromap=0.2.1 bioconda::samtools=1.15" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:ed3529ef5253d7ccbc688b6a4c5c447152685757-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' :
'quay.io/biocontainers/mulled-v2-1f09f39f20b1c4ee36581dc81cc323c70e661633:bd74d08a359024829a7aec1638a28607bbcd8a58-0' }"
input:
tuple val(meta), path(reads)

8
modules/chromap/index/main.nf
View file

@ -1,11 +1,11 @@
process CHROMAP_INDEX {
tag '$fasta'
tag "$fasta"
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null)
conda (params.enable_conda ? "bioconda::chromap=0.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' :
'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }"
'https://depot.galaxyproject.org/singularity/chromap:0.2.1--hd03093a_0' :
'quay.io/biocontainers/chromap:0.2.1--hd03093a_0' }"
input:
path fasta

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

@ -41,7 +41,7 @@ process CONTROLFREEC_FREEC {
def chr_length = fai ? "chrLenFile = \${PWD}/${fai}" : ""
def breakpointthreshold = task.ext.args?["general"]?["breakpointthreshold"] ? "breakPointThreshold = ${task.ext.args["general"]["breakpointthreshold"]}" : ""
def breakpointtype = task.ext.args?["general"]?["breakpointtype"] ? "breakPointType = ${task.ext.args["general"]["breakpointtype"]}" : ""
def coefficientofvariation = task.ext.args?["general"]?["coefficient"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : ""
def coefficientofvariation = task.ext.args?["general"]?["coefficientofvariation"] ? "coefficientOfVariation = ${task.ext.args["general"]["coefficientofvariation"]}" : ""
def contamination = task.ext.args?["general"]?["contamination"] ? "contamination = ${task.ext.args["general"]["contamination"]}" : ""
def contaminationadjustment = task.ext.args?["general"]?["contaminationadjustment"] ? "contaminationAdjustment = ${task.ext.args["general"]["contaminationadjustment"]}" : ""
def degree = task.ext.args?["general"]?["degree"] ? "degree = ${task.ext.args["general"]["degree"]}" : ""

8
tests/modules/chromap/chromap/test.yml
View file

@ -8,7 +8,7 @@
- path: output/chromap/test.bed.gz
md5sum: 25e40bde24c7b447292cd68573728694
- path: output/chromap/versions.yml
md5sum: 2d3d2959ac20d98036807964896829e7
md5sum: d24cfc35ad958206a5bc5694221b4fae
- name: chromap chromap test_chromap_chromap_paired_end
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -20,7 +20,7 @@
- path: output/chromap/test.bed.gz
md5sum: 7cdc8448882b75811e0c784f5f20aef2
- path: output/chromap/versions.yml
md5sum: 51cff66779161d8a602cce5989017395
md5sum: 68ffe268a9d460956de4aad2a55ffd68
- name: chromap chromap test_chromap_chromap_paired_bam
command: nextflow run ./tests/modules/chromap/chromap -entry test_chromap_chromap_paired_bam -c ./tests/config/nextflow.config -c ./tests/modules/chromap/chromap/nextflow.config
@ -30,6 +30,6 @@
files:
- path: output/chromap/genome.index
- path: output/chromap/test.bam
md5sum: f255c7441d5a1f307fc642d2aa19647e
md5sum: df467417407408e42992dc3dd15b22f5
- path: output/chromap/versions.yml
md5sum: f91910c44169549c3923931de5c3afcb
md5sum: ea732b4c6f1312d09745b66c3963dd3f

2
tests/modules/chromap/index/test.yml
View file

@ -6,4 +6,4 @@
files:
- path: output/chromap/genome.index
- path: output/chromap/versions.yml
md5sum: b75dec647f9dc5f4887f36d1db7a9ccd
md5sum: fc5c80190d0622ea3e979e6862f8e32b