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⬆️ update freebayes module #29

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⬆️ update freebayes module #29

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2 changes: 1 addition & 1 deletion modules/cnr-ibba/freebayes/chunk/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::freebayes=1.3.6
- bioconda::freebayes=1.3.7
4 changes: 2 additions & 2 deletions modules/cnr-ibba/freebayes/chunk/main.nf
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Expand Up @@ -6,8 +6,8 @@ process FREEBAYES_CHUNK {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0':
'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
'https://depot.galaxyproject.org/singularity/freebayes:1.3.7--h1870644_0':
'biocontainers/freebayes:1.3.7--h1870644_0' }"

input:
tuple val(meta), val(region)
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2 changes: 1 addition & 1 deletion modules/cnr-ibba/freebayes/multi/environment.yml
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Expand Up @@ -4,6 +4,6 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::freebayes=1.3.6
- bioconda::freebayes=1.3.7
- main::numpy
- main::scipy
2 changes: 1 addition & 1 deletion modules/cnr-ibba/freebayes/multi/main.nf
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Expand Up @@ -4,7 +4,7 @@ process FREEBAYES_MULTI {
label 'process_high'

conda "${moduleDir}/environment.yml"
container "docker.io/bunop/freebayes:v0.1"
container "docker.io/bunop/freebayes:v0.2"

input:
tuple val(meta), path(bam)
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2 changes: 1 addition & 1 deletion modules/cnr-ibba/freebayes/single/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::freebayes=1.3.6
- bioconda::freebayes=1.3.7
4 changes: 2 additions & 2 deletions modules/cnr-ibba/freebayes/single/main.nf
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Expand Up @@ -5,8 +5,8 @@ process FREEBAYES_SINGLE {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hb089aa1_0':
'biocontainers/freebayes:1.3.6--hb089aa1_0' }"
'https://depot.galaxyproject.org/singularity/freebayes:1.3.7--h1870644_0':
'biocontainers/freebayes:1.3.7--h1870644_0' }"

input:
tuple val(meta), path(bam), path(bai)
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2 changes: 1 addition & 1 deletion modules/cnr-ibba/freebayes/splitbam/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,6 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::freebayes=1.3.6
- bioconda::freebayes=1.3.7
- main::numpy
- main::scipy
4 changes: 2 additions & 2 deletions modules/cnr-ibba/freebayes/splitbam/main.nf
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Expand Up @@ -4,7 +4,7 @@ process FREEBAYES_SPLITBAM {
label 'process_single'

conda "${moduleDir}/environment.yml"
container "docker.io/bunop/freebayes:v0.1"
container "docker.io/bunop/freebayes:v0.2"

input:
tuple val(meta), path(bam)
Expand All @@ -25,7 +25,7 @@ process FREEBAYES_SPLITBAM {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
ls $bam | xargs -n1 > ${prefix}.list.txt
ls $bam | sort | xargs -n1 > ${prefix}.list.txt

split_ref_by_bai_datasize.py \\
--bam-list ${prefix}.list.txt \\
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4 changes: 2 additions & 2 deletions tests/modules/cnr-ibba/freebayes/chunk/test.yml
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Expand Up @@ -9,6 +9,6 @@
- path: output/freebayes/all.fb.regions.txt
md5sum: e4cd6cbdb91d5205fcefcc7bc068d3e5
- path: output/freebayes/chr22:0-40001.vcf.gz
md5sum: fba544980eebf86c66460c40f48d7809
md5sum: 709872fc2910431b1e8b7074bfe38c67
- path: output/freebayes/chr22:0-40001.vcf.gz.tbi
md5sum: 83b1d5e5b36d61529d9d2d69cd4babc5
md5sum: 4cb176febbc8c26d717a6c6e67b9c905
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