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Make extractcoords subunits splitting a parameter in rrna_extraction swf, also update more modules #112

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Merged
chrisAta merged 4 commits into from
Oct 6, 2025
Merged

Make extractcoords subunits splitting a parameter in rrna_extraction swf, also update more modules #112

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dee1307
make separate_subunits an argument in the rrna_extraction swf as well
chrisAta Oct 6, 2025
31202bc
update pimento version in pimento/generatebcv
chrisAta Oct 6, 2025
2ce9d8f
update snapshot for fastqsuffixheadercheck after updating mpt version
chrisAta Oct 6, 2025
ac5436f
update mpt fpr mapseq2biom and snapshot
chrisAta Oct 6, 2025
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2 changes: 1 addition & 1 deletion modules/ebi-metagenomics/fastqsuffixheadercheck/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,4 +5,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::mgnify-pipelines-toolkit=0.1.6"
- "bioconda::mgnify-pipelines-toolkit=1.2.11"
4 changes: 2 additions & 2 deletions modules/ebi-metagenomics/fastqsuffixheadercheck/main.nf
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Expand Up @@ -5,8 +5,8 @@ process FASTQSUFFIXHEADERCHECK {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mgnify-pipelines-toolkit:1.2.1--pyhdfd78af_0':
'biocontainers/mgnify-pipelines-toolkit:1.2.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/mgnify-pipelines-toolkit:1.2.11--pyhdfd78af_0':
'biocontainers/mgnify-pipelines-toolkit:1.2.11--pyhdfd78af_0' }"

input:
tuple val(meta), path(fastq)
Expand Down
32 changes: 16 additions & 16 deletions modules/ebi-metagenomics/fastqsuffixheadercheck/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@
]
],
"1": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
],
"json": [
[
Expand All @@ -24,15 +24,15 @@
]
],
"versions": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T11:33:28.905264"
"timestamp": "2025-10-06T12:18:34.357361"
},
"fastqsuffixheadercheck - pass - PE": {
"content": [
Expand All @@ -47,7 +47,7 @@
]
],
"1": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
],
"json": [
[
Expand All @@ -59,15 +59,15 @@
]
],
"versions": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T11:33:20.985434"
"timestamp": "2025-10-06T12:18:26.059076"
},
"fastqsuffixheadercheck - pass - SE": {
"content": [
Expand All @@ -82,7 +82,7 @@
]
],
"1": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
],
"json": [
[
Expand All @@ -94,15 +94,15 @@
]
],
"versions": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T11:33:13.151863"
"timestamp": "2025-10-06T12:18:17.779594"
},
"fastqsuffixheadercheck - stub": {
"content": [
Expand All @@ -117,7 +117,7 @@
]
],
"1": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
],
"json": [
[
Expand All @@ -129,14 +129,14 @@
]
],
"versions": [
"versions.yml:md5,3c3c2c79df154c1f2b1bfffb28209a2f"
"versions.yml:md5,89bbadeb55d7a865b8fe633dfdef49e3"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T11:33:36.574452"
"timestamp": "2025-10-06T12:18:41.982063"
}
}
2 changes: 1 addition & 1 deletion modules/ebi-metagenomics/mapseq2biom/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,4 +6,4 @@ channels:
- bioconda
- defaults
dependencies:
- "bioconda::mgnify-pipelines-toolkit=0.1.1"
- "bioconda::mgnify-pipelines-toolkit=1.2.11"
7 changes: 3 additions & 4 deletions modules/ebi-metagenomics/mapseq2biom/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ process MAPSEQ2BIOM {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mgnify-pipelines-toolkit:0.1.1--pyhdfd78af_0' :
'biocontainers/mgnify-pipelines-toolkit:0.1.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/mgnify-pipelines-toolkit:1.2.11--pyhdfd78af_0' :
'biocontainers/mgnify-pipelines-toolkit:1.2.11--pyhdfd78af_0' }"

input:
tuple val(meta), path(msq)
Expand Down Expand Up @@ -37,12 +37,11 @@ process MAPSEQ2BIOM {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mapseq2biom: 0.1.1
mgnify-pipelines-toolkit: \$(get_mpt_version)
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"

"""
Expand Down
10 changes: 5 additions & 5 deletions modules/ebi-metagenomics/mapseq2biom/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -101,7 +101,7 @@
]
],
"3": [
"versions.yml:md5,d8270f637a909a58d0070c3abc946c52"
"versions.yml:md5,762178a94f67dbd9ae40cbc43b14ba62"
],
"biom_notaxid_out": [
[
Expand Down Expand Up @@ -131,14 +131,14 @@
]
],
"versions": [
"versions.yml:md5,d8270f637a909a58d0070c3abc946c52"
"versions.yml:md5,762178a94f67dbd9ae40cbc43b14ba62"
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.2",
"nextflow": "25.04.7"
},
"timestamp": "2024-04-11T09:35:09.669445"
"timestamp": "2025-10-06T13:41:03.879197"
}
}
2 changes: 1 addition & 1 deletion modules/ebi-metagenomics/pimento/generatebcv/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,4 +4,4 @@ channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::mi-pimento=1.0.1"
- "bioconda::mi-pimento=1.0.2"
4 changes: 2 additions & 2 deletions modules/ebi-metagenomics/pimento/generatebcv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,8 +5,8 @@ process PIMENTO_GENERATEBCV {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mi-pimento:1.0.1--pyhdfd78af_0':
'biocontainers/mi-pimento:1.0.1--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/mi-pimento:1.0.2--pyhdfd78af_0':
'biocontainers/mi-pimento:1.0.2--pyhdfd78af_0' }"

input:
tuple val(meta), val(fwd_flag), val(rev_flag), path(fastq)
Expand Down
30 changes: 15 additions & 15 deletions modules/ebi-metagenomics/pimento/generatebcv/tests/main.nf.test.snap
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Expand Up @@ -14,16 +14,16 @@
[
{
"PIMENTO_GENERATEBCV": {
"mi-pimento": "1.0.1"
"mi-pimento": "1.0.2"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T14:38:12.95981"
"timestamp": "2025-10-06T12:13:04.10164"
},
"pimento/generatebcv - none": {
"content": [
Expand All @@ -40,16 +40,16 @@
[
{
"PIMENTO_GENERATEBCV": {
"mi-pimento": "1.0.1"
"mi-pimento": "1.0.2"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T14:38:04.488138"
"timestamp": "2025-10-06T12:12:54.406761"
},
"pimento/generatebcv - F": {
"content": [
Expand All @@ -66,16 +66,16 @@
[
{
"PIMENTO_GENERATEBCV": {
"mi-pimento": "1.0.1"
"mi-pimento": "1.0.2"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T14:37:46.746505"
"timestamp": "2025-10-06T12:12:34.459818"
},
"pimento/generatebcv - FR": {
"content": [
Expand All @@ -92,16 +92,16 @@
[
{
"PIMENTO_GENERATEBCV": {
"mi-pimento": "1.0.1"
"mi-pimento": "1.0.2"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T14:37:37.09592"
"timestamp": "2025-10-06T12:12:23.653155"
},
"pimento/generatebcv - R": {
"content": [
Expand All @@ -118,15 +118,15 @@
[
{
"PIMENTO_GENERATEBCV": {
"mi-pimento": "1.0.1"
"mi-pimento": "1.0.2"
}
}
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "25.04.7"
},
"timestamp": "2025-06-18T14:37:55.942524"
"timestamp": "2025-10-06T12:12:44.720827"
}
}
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