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Bump HISAT2 version to 2.2.1 in all modules (#2139)

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* Fix broken Quast module and bump MultiQC version in dumpsoftwareversions

* Bump HISAT2 version to 2.2.1

* Remove empty md5sums

* Remove empty md5sums

* Remove empty md5sums
This commit is contained in:
Harshil Patel 2022-09-30 20:34:06 +01:00 committed by GitHub
parent ef585046a0
commit 4eed099a12
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GPG key ID: 4AEE18F83AFDEB23
6 changed files with 6 additions and 10 deletions
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8
modules/hisat2/align/main.nf
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@ -3,10 +3,10 @@ process HISAT2_ALIGN {
label 'process_high' label 'process_high'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.15.1" : null) conda (params.enable_conda ? "bioconda::hisat2=2.2.1 bioconda::samtools=1.15.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' : 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' :
'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' }" 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:38aed4501da19db366dc7c8d52d31d94e760cfaf-0' }"
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads)
@ -25,7 +25,7 @@ process HISAT2_ALIGN {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
def strandedness = '' def strandedness = ''
if (meta.strandedness == 'forward') { if (meta.strandedness == 'forward') {

2
modules/hisat2/build/main.nf
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@ -44,7 +44,7 @@ process HISAT2_BUILD {
log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index." log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check." log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
} }
def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
""" """
mkdir hisat2 mkdir hisat2
$extract_exons $extract_exons

2
modules/hisat2/extractsplicesites/main.nf
View file

@ -20,7 +20,7 @@ process HISAT2_EXTRACTSPLICESITES {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
""" """
hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml

2
tests/modules/hisat2/align/test.yml
View file

@ -7,7 +7,6 @@
- path: output/hisat2/test.hisat2.summary.log - path: output/hisat2/test.hisat2.summary.log
md5sum: 7b8a9e61b7646da1089b041333c41a87 md5sum: 7b8a9e61b7646da1089b041333c41a87
- path: output/hisat2/genome.splice_sites.txt - path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/hisat2/test.bam - path: output/hisat2/test.bam
- path: output/hisat2/hisat2/genome.5.ht2 - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173 md5sum: 91198831aaba993acac1734138c5f173
@ -35,7 +34,6 @@
- path: output/hisat2/test.hisat2.summary.log - path: output/hisat2/test.hisat2.summary.log
md5sum: 9839b31db795958cc4b70711a3414e9c md5sum: 9839b31db795958cc4b70711a3414e9c
- path: output/hisat2/genome.splice_sites.txt - path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/hisat2/test.bam - path: output/hisat2/test.bam
- path: output/hisat2/hisat2/genome.5.ht2 - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173 md5sum: 91198831aaba993acac1734138c5f173

1
tests/modules/hisat2/build_test/test.yml
View file

@ -5,7 +5,6 @@
- hisat2/build - hisat2/build
files: files:
- path: output/hisat2/genome.splice_sites.txt - path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e
- path: output/hisat2/hisat2/genome.5.ht2 - path: output/hisat2/hisat2/genome.5.ht2
md5sum: 91198831aaba993acac1734138c5f173 md5sum: 91198831aaba993acac1734138c5f173
- path: output/hisat2/hisat2/genome.7.ht2 - path: output/hisat2/hisat2/genome.7.ht2

1
tests/modules/hisat2/extractsplicesites/test.yml
View file

@ -5,4 +5,3 @@
- hisat2/extractsplicesites - hisat2/extractsplicesites
files: files:
- path: output/hisat2/genome.splice_sites.txt - path: output/hisat2/genome.splice_sites.txt
md5sum: d41d8cd98f00b204e9800998ecf8427e