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Update tabix and add threads #5999

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merged 2 commits into from
Jul 19, 2024
Merged

Update tabix and add threads #5999

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aba93ac
Update tabix and add threads
fellen31 Jul 19, 2024
cd5632c
fix linting
fellen31 Jul 19, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/tabix/bgzip/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- defaults
dependencies:
- bioconda::tabix=1.11
- bioconda::htslib=1.19.1
- bioconda::htslib=1.20
4 changes: 2 additions & 2 deletions modules/nf-core/tabix/bgzip/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TABIX_BGZIP {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
'biocontainers/htslib:1.19.1--h81da01d_1' }"
'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
'biocontainers/htslib:1.20--h5efdd21_2' }"

input:
tuple val(meta), path(input)
Expand Down
56 changes: 44 additions & 12 deletions modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,10 @@
"content": [
"gzi_compress_test.vcf.gz.gzi"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:52:29.328146"
},
"homo_genome_bedgz_compress": {
Expand All @@ -20,7 +24,7 @@

],
"2": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
],
"gzi": [

Expand All @@ -34,16 +38,24 @@
]
],
"versions": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
]
}
],
"timestamp": "2024-02-19T14:52:12.422209"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:28:34.159992362"
},
"test_stub": {
"content": [
"test_stub.vcf.gz"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:52:20.811489"
},
"sarscov2_vcf_bgzip_compress": {
Expand All @@ -61,7 +73,7 @@

],
"2": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
],
"gzi": [

Expand All @@ -75,11 +87,15 @@
]
],
"versions": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
]
}
],
"timestamp": "2024-02-19T14:52:03.706028"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:28:22.087769106"
},
"sarscov2_vcf_bgzip_compress_gzi": {
"content": [
Expand All @@ -101,7 +117,7 @@
]
],
"2": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
],
"gzi": [
[
Expand All @@ -120,22 +136,34 @@
]
],
"versions": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
]
}
],
"timestamp": "2024-02-19T14:52:29.271494"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:28:57.15091665"
},
"bgzip_test": {
"content": [
"bgzip_test.vcf.gz"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:52:03.768295"
},
"bedgz_test": {
"content": [
"bedgz_test.bed"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:52:12.453855"
},
"sarscov2_vcf_bgzip_compress_stub": {
Expand All @@ -158,7 +186,7 @@
]
],
"2": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
],
"gzi": [
[
Expand All @@ -177,10 +205,14 @@
]
],
"versions": [
"versions.yml:md5,e023292de6ee109a44fc67475d658174"
"versions.yml:md5,753c29916d45debdde52f4ac7c745f61"
]
}
],
"timestamp": "2024-02-19T14:52:20.769619"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:28:45.219404786"
}
}
2 changes: 1 addition & 1 deletion modules/nf-core/tabix/bgziptabix/environment.yml
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- defaults
dependencies:
- bioconda::tabix=1.11
- bioconda::htslib=1.19.1
- bioconda::htslib=1.20
6 changes: 3 additions & 3 deletions modules/nf-core/tabix/bgziptabix/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TABIX_BGZIPTABIX {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
'biocontainers/htslib:1.19.1--h81da01d_1' }"
'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
'biocontainers/htslib:1.20--h5efdd21_2' }"

input:
tuple val(meta), path(input)
Expand All @@ -24,7 +24,7 @@ process TABIX_BGZIPTABIX {
def prefix = task.ext.prefix ?: "${meta.id}"
"""
bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
tabix $args2 ${prefix}.${input.getExtension()}.gz
tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand Down
50 changes: 37 additions & 13 deletions modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,14 +8,14 @@
"id": "tbi_test"
},
"tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
"tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
"tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
]
],
"1": [

],
"2": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [

Expand All @@ -26,15 +26,19 @@
"id": "tbi_test"
},
"tbi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
"tbi_test.bed.gz.tbi:md5,24908545311cf2b7c803c41d716872c4"
"tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
]
],
"versions": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
"timestamp": "2024-02-19T14:50:51.513838"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:29:16.053817543"
},
"sarscov2_bed_csi": {
"content": [
Expand All @@ -48,47 +52,63 @@
"id": "csi_test"
},
"csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
"csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
"csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
]
],
"2": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [
[
{
"id": "csi_test"
},
"csi_test.bed.gz:md5,fe4053cf4de3aebbdfc3be2efb125a74",
"csi_test.bed.gz.csi:md5,e06165ddd34640783728cb07f2558b43"
"csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
]
],
"gz_tbi": [

],
"versions": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
"timestamp": "2024-02-19T14:51:00.513777"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:29:27.667745444"
},
"csi_test": {
"content": [
"csi_test.bed.gz"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:51:00.548801"
},
"csi_stub": {
"content": [
"test.bed.gz"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:51:09.218454"
},
"tbi_test": {
"content": [
"tbi_test.bed.gz"
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-02-19T14:50:51.579654"
},
"sarscov2_bed_csi_stub": {
Expand All @@ -113,7 +133,7 @@
]
],
"2": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
],
"gz_csi": [
[
Expand All @@ -134,10 +154,14 @@
]
],
"versions": [
"versions.yml:md5,b4765e4d896ce4a4cdd6c896d12555fc"
"versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa"
]
}
],
"timestamp": "2024-02-19T14:51:09.164254"
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-19T11:29:45.105209991"
}
}
4 changes: 3 additions & 1 deletion modules/nf-core/tabix/tabix/environment.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
name: tabix_tabix

channels:
- conda-forge
- bioconda
- defaults

dependencies:
- bioconda::htslib=1.20
- bioconda::tabix=1.11
- bioconda::htslib=1.19.1
11 changes: 7 additions & 4 deletions modules/nf-core/tabix/tabix/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ process TABIX_TABIX {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/htslib:1.19.1--h81da01d_1' :
'biocontainers/htslib:1.19.1--h81da01d_1' }"
'https://depot.galaxyproject.org/singularity/htslib:1.20--h5efdd21_2' :
'biocontainers/htslib:1.20--h5efdd21_2' }"

input:
tuple val(meta), path(tab)
Expand All @@ -21,7 +21,10 @@ process TABIX_TABIX {
script:
def args = task.ext.args ?: ''
"""
tabix $args $tab
tabix \\
--threads $task.cpus \\
$args \\
$tab

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -33,8 +36,8 @@ process TABIX_TABIX {
"""
touch ${tab}.tbi
touch ${tab}.csi
cat <<-END_VERSIONS > versions.yml

cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
Expand Down
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