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update bowtie2 v2.5.4 #6870

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update bowtie2 v2.5.4 #6870

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26a3bee
update bowtie2 v2.5.4 in bowtie2/build
LucilleAugusta Oct 28, 2024
1dc72cb
update bowtie2 to v2.5.4 in bowtie2/align
LucilleAugusta Oct 28, 2024
028cb0c
make test have sorted output and grab more lines for md5sum check
fmalmeida Oct 29, 2024
512b457
Merge branch 'master' into 6821-update-module-bowtie2
fmalmeida Oct 29, 2024
0fea1ad
avoid getting header
fmalmeida Oct 29, 2024
970a2f1
Merge branch 'master' into 6821-update-module-bowtie2
atrigila Nov 4, 2024
8c98dd0
Merge branch 'master' into 6821-update-module-bowtie2
fmalmeida Nov 8, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/bowtie2/align/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,6 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::bowtie2=2.5.2
- bioconda::bowtie2=2.5.4
- bioconda::samtools=1.18
- conda-forge::pigz=2.6
4 changes: 2 additions & 2 deletions modules/nf-core/bowtie2/align/main.nf
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Expand Up @@ -4,8 +4,8 @@ process BOWTIE2_ALIGN {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' :
'biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:f70b31a2db15c023d641c32f433fb02cd04df5a6-0' }"
'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :
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Suggested change
'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :
'oras://community.wave.seqera.io/library/bowtie2_samtools_pigz:19e9ad812f803021' :

We're not supporting oras yet. There's a script https://github.com/nf-core/modules/blob/master/.github/scripts/wave_singularity.py for this if anyone beats me to it, just going through Seqera container issues.

'community.wave.seqera.io/library/bowtie2_samtools_pigz:8bde63944b003030' }"

input:
tuple val(meta) , path(reads)
Expand Down
28 changes: 14 additions & 14 deletions modules/nf-core/bowtie2/align/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -81,7 +81,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand All @@ -90,7 +90,7 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.sam[0][1]).readLines()[0..4],
file(process.out.sam[0][1]).readLines()[4..10],
process.out.log,
process.out.fastq,
process.out.versions
Expand Down Expand Up @@ -127,7 +127,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand All @@ -136,7 +136,7 @@ nextflow_process {
assertAll (
{ assert process.success },
{ assert snapshot(
file(process.out.sam[0][1]).readLines()[0..4],
file(process.out.sam[0][1]).readLines()[4..10],
process.out.log,
process.out.fastq,
process.out.versions
Expand Down Expand Up @@ -172,7 +172,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -220,7 +220,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -268,7 +268,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -314,7 +314,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -363,7 +363,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -411,7 +411,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -456,7 +456,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -553,7 +553,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down Expand Up @@ -600,7 +600,7 @@ nextflow_process {
input[1] = BOWTIE2_BUILD.out.index
input[2] = [[ id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)]
input[3] = false //save_unaligned
input[4] = false //sort
input[4] = true //sort
"""
}
}
Expand Down
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