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Pyrodigal - add --jobs flag for multi-threaded operation, bump version #7116

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Merged
prototaxites merged 8 commits into from
Dec 5, 2024
Merged

Pyrodigal - add --jobs flag for multi-threaded operation, bump version #7116

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e25890f
Pyrodigal - add --jobs flag for multi-threaded operation
prototaxites Nov 28, 2024
1e39cd8
Update Pyrodigal container
prototaxites Nov 29, 2024
a5c12bc
Bump conda env
prototaxites Nov 29, 2024
bcdffa2
Merge branch 'master' into master
prototaxites Nov 30, 2024
8190b90
Merge branch 'nf-core:master' into master
prototaxites Dec 2, 2024
43cfba8
Update snapshot
prototaxites Dec 2, 2024
d1261ea
Merge branch 'nf-core:master' into master
prototaxites Dec 5, 2024
205dce0
Update modules/nf-core/pyrodigal/main.nf
prototaxites Dec 5, 2024
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2 changes: 1 addition & 1 deletion modules/nf-core/pyrodigal/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,5 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::pyrodigal=3.3.0
- bioconda::pyrodigal=3.6.3
- conda-forge::pigz=2.8
7 changes: 4 additions & 3 deletions modules/nf-core/pyrodigal/main.nf
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
process PYRODIGAL {
tag "$meta.id"
label 'process_single'
label 'process_medium'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0':
'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:47e7d40834619419f202394563267d74cef857be-0' }"
'https://depot.galaxyproject.org/singularity/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:da1134ad604a59a6f439bdcc3f6df690eba47e9a-0':
'biocontainers/mulled-v2-2fe9a8ce513c91df34b43a6610df94c3a2eb3bd0:da1134ad604a59a6f439bdcc3f6df690eba47e9a-0' }"

input:
tuple val(meta), path(fasta)
Expand All @@ -28,6 +28,7 @@ process PYRODIGAL {
pigz -cdf ${fasta} > pigz_fasta.fna

pyrodigal \\
--jobs ${task.cpus} \\
$args \\
-i pigz_fasta.fna \\
-f $output_format \\
Expand Down
46 changes: 23 additions & 23 deletions modules/nf-core/pyrodigal/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -5,21 +5,21 @@
"test.fna.gz",
"test.faa.gz",
"test.score.gz",
"versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
"versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-03-18T15:42:12.012112014"
"timestamp": "2024-12-02T15:17:12.218638993"
},
"pyrodigal - sarscov2 - gbk": {
"content": [
[
" CDS 310..13476",
" /codon_start=1",
" /inference=\"ab initio prediction:pyrodigal:3.3.0\"",
" /inference=\"ab initio prediction:pyrodigal:3.6.3\"",
" /locus_tag=\"MT192765.1_1\"",
" /transl_table=11",
" /translation=\"MPVLQVRDVLVRGFGDSVEEVLSEARQHLKDGTCGLVEVEKGVLP",
Expand Down Expand Up @@ -51,18 +51,18 @@
"id": "test",
"single_end": false
},
"test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
"test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
]
],
[
"versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
"versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.3"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-07-30T06:09:40.289778252"
"timestamp": "2024-12-02T15:17:01.228814939"
},
"pyrodigal - sarscov2 - gff": {
"content": [
Expand All @@ -73,7 +73,7 @@
"id": "test",
"single_end": false
},
"test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27"
"test.gff.gz:md5,898c1e24e71fa108981597b8bb32110f"
]
],
"1": [
Expand All @@ -100,19 +100,19 @@
"id": "test",
"single_end": false
},
"test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
"test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
]
],
"4": [
"versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
"versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
],
"annotations": [
[
{
"id": "test",
"single_end": false
},
"test.gff.gz:md5,8fcd2d93131cf9fb0c82b81db059ad27"
"test.gff.gz:md5,898c1e24e71fa108981597b8bb32110f"
]
],
"faa": [
Expand All @@ -139,33 +139,33 @@
"id": "test",
"single_end": false
},
"test.score.gz:md5,c0703a9e662ae0b21c7bbb082ef3fb5f"
"test.score.gz:md5,63e6975e705be1fe749eb54bd4ea478e"
]
],
"versions": [
"versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
"versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-03-18T15:41:55.822235843"
"timestamp": "2024-12-02T15:16:49.907998584"
},
"pyrodigal - sarscov2 - gbk - stub": {
"content": [
[
"test.fna.gz",
"test.faa.gz",
"test.score.gz",
"versions.yml:md5,4aab54554829148e01cc0dc7bf6cb5d3"
"versions.yml:md5,296cc4ed71c8eb16bbc6978fe6299b77"
]
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "24.10.2"
},
"timestamp": "2024-03-18T15:42:19.81157751"
"timestamp": "2024-12-02T15:17:22.681680508"
}
}