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Fix release lints from template 3.3.1 #95

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Merged
itrujnara merged 6 commits into from
Jun 17, 2025
Merged

Fix release lints from template 3.3.1 #95

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4d8afe8
Enable custom configs
itrujnara Jun 17, 2025
4d5aab9
Replace mulled containers with Seqera Containers
itrujnara Jun 17, 2025
e56ecce
Update DIAMOND/CLUSTER module
itrujnara Jun 17, 2025
ef1373b
Update DIAMOND/CLUSTER again
itrujnara Jun 17, 2025
04a3397
Fix nf-test config to skip testing nf-core modules
itrujnara Jun 17, 2025
c06a94a
Update test snapshot after module update
itrujnara Jun 17, 2025
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -22,7 +22,7 @@
},
"diamond/cluster": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"git_sha": "cb774ba4a9c79de334a71f802680cb66f3c8515e",
"installed_by": ["modules"]
},
"gawk": {
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4 changes: 2 additions & 2 deletions modules/local/fetch_ensembl_sequences.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_ENSEMBL_SEQUENCES {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(ids), path(query_fasta)
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4 changes: 2 additions & 2 deletions modules/local/fetch_inspector_group_online.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_INSPECTOR_GROUP_ONLINE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(uniprot_id), path(taxid), path(exact)
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4 changes: 2 additions & 2 deletions modules/local/fetch_oma_group_online.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_OMA_GROUP_ONLINE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(uniprot_id), path(taxid), path(exact)
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4 changes: 2 additions & 2 deletions modules/local/fetch_oma_sequences.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_OMA_SEQUENCES {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(ids), path(query_fasta)
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4 changes: 2 additions & 2 deletions modules/local/fetch_panther_group_online.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_PANTHER_GROUP_ONLINE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(uniprot_id), path(taxid), path(exact)
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4 changes: 2 additions & 2 deletions modules/local/fetch_refseq_sequences.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_REFSEQ_SEQUENCES {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(ids), path(query_fasta)
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4 changes: 2 additions & 2 deletions modules/local/fetch_uniprot_sequences.nf
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Expand Up @@ -4,8 +4,8 @@ process FETCH_UNIPROT_SEQUENCES {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(ids), path(query_fasta)
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4 changes: 2 additions & 2 deletions modules/local/filter_fasta.nf
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Expand Up @@ -4,8 +4,8 @@ process FILTER_FASTA {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(fasta), path(structures)
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4 changes: 2 additions & 2 deletions modules/local/filter_hits.nf
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Expand Up @@ -4,8 +4,8 @@ process FILTER_HITS {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(score_table), path(queryid)
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4 changes: 2 additions & 2 deletions modules/local/identify_seq_online.nf
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Expand Up @@ -4,8 +4,8 @@ process IDENTIFY_SEQ_ONLINE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(fasta)
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4 changes: 2 additions & 2 deletions modules/local/make_hits_table.nf
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Expand Up @@ -4,8 +4,8 @@ process MAKE_HITS_TABLE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(merged_csv)
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4 changes: 2 additions & 2 deletions modules/local/make_merge_table.nf
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Expand Up @@ -4,8 +4,8 @@ process MAKE_MERGE_TABLE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(clusters)
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4 changes: 2 additions & 2 deletions modules/local/make_score_table.nf
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Expand Up @@ -4,8 +4,8 @@ process MAKE_SCORE_TABLE {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(merged_csv), path(id_map)
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4 changes: 2 additions & 2 deletions modules/local/make_stats.nf
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Expand Up @@ -4,8 +4,8 @@ process MAKE_STATS {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), path(score_table)
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4 changes: 2 additions & 2 deletions modules/local/write_seqinfo.nf
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Expand Up @@ -4,8 +4,8 @@ process WRITE_SEQINFO {

conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' :
'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }"
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' :
'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }"

input:
tuple val(meta), val(uniprot_id)
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2 changes: 1 addition & 1 deletion modules/nf-core/diamond/cluster/environment.yml
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24 changes: 12 additions & 12 deletions modules/nf-core/diamond/cluster/main.nf
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5 changes: 5 additions & 0 deletions modules/nf-core/diamond/cluster/meta.yml
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38 changes: 19 additions & 19 deletions modules/nf-core/diamond/cluster/tests/main.nf.test.snap
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2 changes: 0 additions & 2 deletions modules/nf-core/diamond/cluster/tests/tags.yml
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This file was deleted.

3 changes: 1 addition & 2 deletions nextflow.config
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Expand Up @@ -209,8 +209,7 @@ includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !pa


// Load nf-core/reportho custom profiles from different institutions.
// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
// includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/reportho.config" : "/dev/null"
includeConfig params.custom_config_base && (!System.getenv('NXF_OFFLINE') || !params.custom_config_base.startsWith('http')) ? "${params.custom_config_base}/pipeline/reportho.config" : "/dev/null"

// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
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2 changes: 1 addition & 1 deletion nf-test.config
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Expand Up @@ -8,7 +8,7 @@ config {

configFile "tests/nextflow.config"

ignore "modules/*"
ignore "modules/nf-core/**"

profile "docker"

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