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Merged
mberacochea merged 14 commits into from
May 14, 2026
Merged

Update m+s #64

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34728e8
Template update for nf-core/tools version 4.0.0
nf-core-bot Apr 28, 2026
96dee61
Template update for nf-core/tools version 4.0.2
nf-core-bot Apr 30, 2026
4a5d25b
Merge branch 'nf-core-template-merge-4.0.2' into dev
vagkaratzas May 7, 2026
de341c7
adding to template merge
vagkaratzas May 7, 2026
9deec0e
m + s updates to latest
vagkaratzas May 7, 2026
6106618
replace fastavalidator
KateSakharova May 7, 2026
5f581b7
add failed to report
KateSakharova May 7, 2026
51308e9
Add arm64 configs (prep for biocontainers migration) -- updated snaps
mberacochea May 13, 2026
0892ccf
nf-core linting - modules.json formatting
mberacochea May 13, 2026
a95b77d
Ignore container_configs when linting the pipeline
mberacochea May 13, 2026
1c3f3bf
fixes after review
KateSakharova May 14, 2026
1a293a6
Merge branch 'dev' into update-m+s
KateSakharova May 14, 2026
f65ab00
fixes after review
KateSakharova May 14, 2026
542f1c1
Regenerate tests snapshots
mberacochea May 14, 2026
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1 change: 1 addition & 0 deletions .nf-core.yml
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@@ -1,4 +1,5 @@
lint:
container_configs: false
files_exist:
- conf/igenomes.config
- conf/igenomes_ignored.config
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1 change: 1 addition & 0 deletions conf/containers_docker_arm64.config
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@@ -1 +1,2 @@
process { withName: 'MULTIQC' { container = 'community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136' } }
process { withName: 'FALINT' { container = 'community.wave.seqera.io/library/fa-lint:1.2.0--f51af98c5c777a31'} }
1 change: 1 addition & 0 deletions conf/containers_singularity_https_arm64.config
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@@ -1 +1,2 @@
process { withName: 'MULTIQC' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data' } }
process { withName: 'FALINT' { container = 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9d/9d381ce77aaeeb2c5d7af44af33f1456498cff3a7e73625649bb633a2bb686fa/data' } }
1 change: 1 addition & 0 deletions conf/containers_singularity_oras_arm64.config
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@@ -1 +1,2 @@
process { withName: 'MULTIQC' { container = 'oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726' } }
process { withName: 'FALINT' { container = 'oras://community.wave.seqera.io/library/fa-lint:1.2.0--dd5a4a2b8726afe7' } }
2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -23,7 +23,7 @@ process {
// VALIDATION OF INPUT FASTA FILES
//

withName: 'FASTAVALIDATOR' {
withName: 'FALINT' {
publishDir = [
enabled: false
]
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2 changes: 0 additions & 2 deletions main.nf
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Expand Up @@ -58,7 +58,6 @@ workflow NFCORE_SEQSUBMIT {
params.centre_name,
params.upload_tpa,
params.test_upload,
params.webin_cli_version,
params.webincli_mode
)
ch_multiqc_report = GENOMESUBMIT.out.multiqc_report
Expand All @@ -73,7 +72,6 @@ workflow NFCORE_SEQSUBMIT {
params.study_metadata,
params.upload_tpa,
params.test_upload,
params.webin_cli_version,
params.webincli_mode
)
ch_multiqc_report = ASSEMBLYSUBMIT.out.multiqc_report
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37 changes: 18 additions & 19 deletions modules.json
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Expand Up @@ -7,64 +7,63 @@
"nf-core": {
"barrnap": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"catpack/addnames": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"catpack/bins": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"catpack/contigs": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"catpack/download": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"catpack/prepare": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"catpack/summarise": {
"branch": "master",
"git_sha": "1100099613c12e944931426f46f10b14c4a74b3d",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
},
"checkm2/databasedownload": {
"branch": "master",
"git_sha": "81470b59ebadb3d01dcfcd37d44f88eb890f4851",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"checkm2/predict": {
"branch": "master",
"git_sha": "81470b59ebadb3d01dcfcd37d44f88eb890f4851",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"coverm/contig": {
"branch": "master",
"git_sha": "27e31681fdbf1e511257355a236037a8cd9c2b2e",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"coverm/genome": {
"branch": "master",
"git_sha": "8583516e8bdf15b48539c085fea9db657e814a30",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["modules"]
},
"fastavalidator": {
"falint": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"],
"patch": "modules/nf-core/fastavalidator/fastavalidator.diff"
"git_sha": "f4952081c36cd091ef1693e7f0b11d8569ae5107",
"installed_by": ["modules"]
},
"find/concatenate": {
"branch": "master",
Expand All @@ -79,12 +78,12 @@
},
"trnascanse": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "0c739827833fdece07eb80618fd085a9a8992406",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
"git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",
"installed_by": ["fasta_classify_catpack"]
}
}
Expand All @@ -99,7 +98,7 @@
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "1a545fcbd762911c21a64ced3dbef99b2b51ac75",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
Expand All @@ -109,7 +108,7 @@
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
"git_sha": "ce3424257de288c0ca25f097a68d3a289da23f12",
"installed_by": ["subworkflows"]
}
}
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17 changes: 3 additions & 14 deletions modules/nf-core/barrnap/main.nf
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37 changes: 27 additions & 10 deletions modules/nf-core/barrnap/meta.yml
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10 changes: 4 additions & 6 deletions modules/nf-core/barrnap/tests/main.nf.test
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44 changes: 30 additions & 14 deletions modules/nf-core/barrnap/tests/main.nf.test.snap
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4 changes: 2 additions & 2 deletions modules/nf-core/catpack/addnames/main.nf
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4 changes: 2 additions & 2 deletions modules/nf-core/catpack/bins/main.nf
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