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mulled biocontainer for vardict-java and htslib #5920

Merged
merged 9 commits into from
Jul 5, 2024
Merged

mulled biocontainer for vardict-java and htslib #5920

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d63cb5a
vardict-java bgzip mulled container
eolaniru Jul 4, 2024
2170619
update bioconda env
eolaniru Jul 4, 2024
92a1f40
code polishing
eolaniru Jul 4, 2024
ce3c246
Update modules/nf-core/vardictjava/main.nf
eolaniru Jul 4, 2024
a76a214
args3 for bgzip
eolaniru Jul 4, 2024
5e6a40a
args3
eolaniru Jul 4, 2024
911cabd
Update snap
SPPearce Jul 4, 2024
351e7c9
Merge branch 'master' into patch-1
nvnieuwk Jul 5, 2024
9f6b3ab
removed whitespace
eolaniru Jul 5, 2024
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1 change: 1 addition & 0 deletions modules/nf-core/vardictjava/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,5 @@ channels:
- bioconda
- defaults
dependencies:
- bioconda::htslib=1.20
- bioconda::vardict-java=1.8.3
12 changes: 7 additions & 5 deletions modules/nf-core/vardictjava/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,16 @@ process VARDICTJAVA {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
'biocontainers/vardict-java:1.8.3--hdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' :
'biocontainers/mulled-v2-731b8c4cf44d76e9aa181af565b9eee448d82a8c:edd70e76f3529411a748168f6eb1a61f29702123-0' }"

input:
tuple val(meta), path(bams), path(bais), path(bed)
tuple val(meta2), path(fasta)
tuple val(meta3), path(fasta_fai)

output:
tuple val(meta), path("*.vcf"), emit: vcf
tuple val(meta), path("*.vcf.gz"), emit: vcf
path "versions.yml" , emit: versions

when:
Expand All @@ -22,6 +22,7 @@ process VARDICTJAVA {
script:
def args = task.ext.args ?: '-c 1 -S 2 -E 3'
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

def somatic = bams instanceof List && bams.size() == 2 ? true : false
Expand All @@ -39,7 +40,7 @@ process VARDICTJAVA {
| ${filter} \\
| ${convert_to_vcf} \\
${args2} \\
> ${prefix}.vcf
| bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -51,10 +52,11 @@ process VARDICTJAVA {
stub:
def args = task.ext.args ?: '-c 1 -S 2 -E 3'
def args2 = task.ext.args2 ?: ''
def args3 = task.ext.args3 ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}.vcf
echo '' | gzip > ${prefix}.vcf.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
16 changes: 8 additions & 8 deletions modules/nf-core/vardictjava/tests/main.nf.test.snap
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Expand Up @@ -7,7 +7,7 @@
{
"id": "test"
},
"test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e"
"test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
]
],
"1": [
Expand All @@ -18,7 +18,7 @@
{
"id": "test"
},
"test.vcf:md5,e8411ecae49b4f6afa6ea0b681ea506e"
"test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e"
]
],
"versions": [
Expand All @@ -28,9 +28,9 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2023-10-24T09:24:20.923172332"
"timestamp": "2024-07-04T19:08:38.328190023"
},
"homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": {
"content": [
Expand All @@ -40,7 +40,7 @@
{
"id": "test"
},
"test.vcf:md5,b52c874c18be636d876d1e0df4a449c3"
"test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
]
],
"1": [
Expand All @@ -51,7 +51,7 @@
{
"id": "test"
},
"test.vcf:md5,b52c874c18be636d876d1e0df4a449c3"
"test.vcf.gz:md5,b52c874c18be636d876d1e0df4a449c3"
]
],
"versions": [
Expand All @@ -61,8 +61,8 @@
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nextflow": "24.04.2"
},
"timestamp": "2024-05-15T05:05:37.320114013"
"timestamp": "2024-07-04T19:08:54.416661915"
}
}
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