From 4d8afe8cab3776ad2e4c4f22d4a89a8712b3527c Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 14:29:21 +0200 Subject: [PATCH 1/6] Enable custom configs --- nextflow.config | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 165e601..5a1bc58 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 From 4d5aab9e3d81d8f53bac366477020c2833b3f09c Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 14:42:26 +0200 Subject: [PATCH 2/6] Replace mulled containers with Seqera Containers This fixes the download test in CI --- modules/local/fetch_ensembl_sequences.nf | 4 ++-- modules/local/fetch_inspector_group_online.nf | 4 ++-- modules/local/fetch_oma_group_online.nf | 4 ++-- modules/local/fetch_oma_sequences.nf | 4 ++-- modules/local/fetch_panther_group_online.nf | 4 ++-- modules/local/fetch_refseq_sequences.nf | 4 ++-- modules/local/fetch_uniprot_sequences.nf | 4 ++-- modules/local/filter_fasta.nf | 4 ++-- modules/local/filter_hits.nf | 4 ++-- modules/local/identify_seq_online.nf | 4 ++-- modules/local/make_hits_table.nf | 4 ++-- modules/local/make_merge_table.nf | 4 ++-- modules/local/make_score_table.nf | 4 ++-- modules/local/make_stats.nf | 4 ++-- modules/local/write_seqinfo.nf | 4 ++-- 15 files changed, 30 insertions(+), 30 deletions(-) diff --git a/modules/local/fetch_ensembl_sequences.nf b/modules/local/fetch_ensembl_sequences.nf index 25ee910..956198a 100644 --- a/modules/local/fetch_ensembl_sequences.nf +++ b/modules/local/fetch_ensembl_sequences.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(ids), path(query_fasta) diff --git a/modules/local/fetch_inspector_group_online.nf b/modules/local/fetch_inspector_group_online.nf index 6bf1708..5a44287 100644 --- a/modules/local/fetch_inspector_group_online.nf +++ b/modules/local/fetch_inspector_group_online.nf @@ -4,8 +4,8 @@ process FETCH_INSPECTOR_GROUP_ONLINE { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/fetch_oma_group_online.nf b/modules/local/fetch_oma_group_online.nf index 70f2fd9..4b732ed 100644 --- a/modules/local/fetch_oma_group_online.nf +++ b/modules/local/fetch_oma_group_online.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(uniprot_id), path(taxid), path(exact) diff --git a/modules/local/fetch_oma_sequences.nf b/modules/local/fetch_oma_sequences.nf index 0a8dc7f..bac1563 100644 --- a/modules/local/fetch_oma_sequences.nf +++ b/modules/local/fetch_oma_sequences.nf @@ -4,8 +4,8 @@ process FETCH_OMA_SEQUENCES { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/fetch_panther_group_online.nf b/modules/local/fetch_panther_group_online.nf index 972699c..7a57d27 100644 --- a/modules/local/fetch_panther_group_online.nf +++ b/modules/local/fetch_panther_group_online.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(uniprot_id), path(taxid), path(exact) diff --git a/modules/local/fetch_refseq_sequences.nf b/modules/local/fetch_refseq_sequences.nf index f583f54..0ba1dc5 100644 --- a/modules/local/fetch_refseq_sequences.nf +++ b/modules/local/fetch_refseq_sequences.nf @@ -4,8 +4,8 @@ process FETCH_REFSEQ_SEQUENCES { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/fetch_uniprot_sequences.nf b/modules/local/fetch_uniprot_sequences.nf index ed64573..a38da54 100644 --- a/modules/local/fetch_uniprot_sequences.nf +++ b/modules/local/fetch_uniprot_sequences.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(ids), path(query_fasta) diff --git a/modules/local/filter_fasta.nf b/modules/local/filter_fasta.nf index 02026e2..ef5050a 100644 --- a/modules/local/filter_fasta.nf +++ b/modules/local/filter_fasta.nf @@ -4,8 +4,8 @@ process FILTER_FASTA { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/filter_hits.nf b/modules/local/filter_hits.nf index 9cd3038..cc64774 100644 --- a/modules/local/filter_hits.nf +++ b/modules/local/filter_hits.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(score_table), path(queryid) diff --git a/modules/local/identify_seq_online.nf b/modules/local/identify_seq_online.nf index 76b7b85..9aab7f0 100644 --- a/modules/local/identify_seq_online.nf +++ b/modules/local/identify_seq_online.nf @@ -4,8 +4,8 @@ process IDENTIFY_SEQ_ONLINE { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/make_hits_table.nf b/modules/local/make_hits_table.nf index 3651aac..e143edc 100644 --- a/modules/local/make_hits_table.nf +++ b/modules/local/make_hits_table.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(merged_csv) diff --git a/modules/local/make_merge_table.nf b/modules/local/make_merge_table.nf index d0e663a..18b2b8f 100644 --- a/modules/local/make_merge_table.nf +++ b/modules/local/make_merge_table.nf @@ -4,8 +4,8 @@ process MAKE_MERGE_TABLE { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/make_score_table.nf b/modules/local/make_score_table.nf index 118025d..1a91fee 100644 --- a/modules/local/make_score_table.nf +++ b/modules/local/make_score_table.nf @@ -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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' : - 'biocontainers/mulled-v2-bc54124b36864a4af42a9db48b90a404b5869e7e:5258b8e5ba20587b7cbf3e942e973af5045a1e59-0' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/6b/6b2900901bc81cfb5d255a250ee196f4e2f8707ba6de704178eb40151fd849f8/data' : + 'community.wave.seqera.io/library/biopython_python_requests:ba620bb488048968' }" input: tuple val(meta), path(merged_csv), path(id_map) diff --git a/modules/local/make_stats.nf b/modules/local/make_stats.nf index 764b78d..cbf2723 100644 --- a/modules/local/make_stats.nf +++ b/modules/local/make_stats.nf @@ -4,8 +4,8 @@ process MAKE_STATS { conda "conda-forge::python=3.11.0 conda-forge::biopython=1.83.0 conda-forge::requests=2.31.0" container "${ 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) diff --git a/modules/local/write_seqinfo.nf b/modules/local/write_seqinfo.nf index 3c67549..23f9403 100644 --- a/modules/local/write_seqinfo.nf +++ b/modules/local/write_seqinfo.nf @@ -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) From e56ecce45216d6de1c9db00e53041a4b408dd060 Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 14:46:58 +0200 Subject: [PATCH 3/6] Update DIAMOND/CLUSTER module --- modules.json | 2 +- .../nf-core/diamond/cluster/environment.yml | 2 +- modules/nf-core/diamond/cluster/main.nf | 24 ++++++------ modules/nf-core/diamond/cluster/meta.yml | 5 +++ .../diamond/cluster/tests/main.nf.test.snap | 38 +++++++++---------- .../nf-core/diamond/cluster/tests/tags.yml | 2 - 6 files changed, 38 insertions(+), 35 deletions(-) delete mode 100644 modules/nf-core/diamond/cluster/tests/tags.yml diff --git a/modules.json b/modules.json index 1070756..5b9509e 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "diamond/cluster": { "branch": "master", - "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", + "git_sha": "aecbc87790ee51c0b24fffa13aa2f34dfdd105f5", "installed_by": ["modules"] }, "gawk": { diff --git a/modules/nf-core/diamond/cluster/environment.yml b/modules/nf-core/diamond/cluster/environment.yml index 216da62..18ad677 100644 --- a/modules/nf-core/diamond/cluster/environment.yml +++ b/modules/nf-core/diamond/cluster/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::diamond=2.1.9" + - bioconda::diamond=2.1.12 diff --git a/modules/nf-core/diamond/cluster/main.nf b/modules/nf-core/diamond/cluster/main.nf index db12d51..0679ba7 100644 --- a/modules/nf-core/diamond/cluster/main.nf +++ b/modules/nf-core/diamond/cluster/main.nf @@ -1,34 +1,34 @@ process DIAMOND_CLUSTER { - tag "$meta.id" + tag "${meta.id}" label 'process_medium' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/diamond:2.1.9--h43eeafb_0': - 'biocontainers/diamond:2.1.9--h43eeafb_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/diamond:2.1.12--hdb4b4cc_1' + : 'biocontainers/diamond:2.1.12--hdb4b4cc_1'}" input: tuple val(meta), path(db) output: tuple val(meta), path("*.tsv"), emit: tsv - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def mem = task.memory.toKilo() + 'K' + def mem = task.memory.toKilo() + 'K' def memarg = "-M ${mem}" """ diamond \\ cluster \\ - $args \\ - $memarg \\ - -p $task.cpus \\ - -d $db \\ + ${args} \\ + ${memarg} \\ + -p ${task.cpus} \\ + -d ${db} \\ -o ${prefix}.tsv cat <<-END_VERSIONS > versions.yml @@ -38,7 +38,7 @@ process DIAMOND_CLUSTER { """ stub: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ touch ${prefix}.tsv diff --git a/modules/nf-core/diamond/cluster/meta.yml b/modules/nf-core/diamond/cluster/meta.yml index 49699ce..ee1ce1a 100644 --- a/modules/nf-core/diamond/cluster/meta.yml +++ b/modules/nf-core/diamond/cluster/meta.yml @@ -27,6 +27,8 @@ input: description: The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format. pattern: "*.{dmnd,fa,faa,fasta}(.gz)" + ontologies: + - edam: http://edamontology.org/format_1929 # FASTA output: - tsv: - meta: @@ -39,11 +41,14 @@ output: description: a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column pattern: "*.tsv" + ontologies: [] - versions: - versions.yml: type: file description: File containing software versions pattern: "versions.yml" + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@itrujnara" maintainers: diff --git a/modules/nf-core/diamond/cluster/tests/main.nf.test.snap b/modules/nf-core/diamond/cluster/tests/main.nf.test.snap index 9b4ec99..03e9056 100644 --- a/modules/nf-core/diamond/cluster/tests/main.nf.test.snap +++ b/modules/nf-core/diamond/cluster/tests/main.nf.test.snap @@ -7,30 +7,30 @@ { "id": "human" }, - "human.tsv:md5,b86602979f73d25280979ae31c6cedf5" + "human.tsv:md5,4c86d0af520411f4b19dd482ede06f9e" ] ], "1": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ], "tsv": [ [ { "id": "human" }, - "human.tsv:md5,b86602979f73d25280979ae31c6cedf5" + "human.tsv:md5,4c86d0af520411f4b19dd482ede06f9e" ] ], "versions": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.2" }, - "timestamp": "2024-07-26T12:47:43.215388" + "timestamp": "2025-06-05T10:54:18.541054211" }, "human - dmnd": { "content": [ @@ -40,30 +40,30 @@ { "id": "human" }, - "human.tsv:md5,b86602979f73d25280979ae31c6cedf5" + "human.tsv:md5,4c86d0af520411f4b19dd482ede06f9e" ] ], "1": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ], "tsv": [ [ { "id": "human" }, - "human.tsv:md5,b86602979f73d25280979ae31c6cedf5" + "human.tsv:md5,4c86d0af520411f4b19dd482ede06f9e" ] ], "versions": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.2" }, - "timestamp": "2024-07-26T12:48:18.237846" + "timestamp": "2025-06-05T10:56:40.730903546" }, "human - fasta - stub": { "content": [ @@ -78,7 +78,7 @@ ] ], "1": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ], "tsv": [ [ @@ -90,14 +90,14 @@ ] ], "versions": [ - "versions.yml:md5,e4c7a66a72f105348f32bbe145bf4418" + "versions.yml:md5,f266dd13f0f75002ce547ad8c69cfced" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "25.04.2" }, - "timestamp": "2024-07-26T13:03:23.494583" + "timestamp": "2025-06-05T10:56:53.444291997" } } \ No newline at end of file diff --git a/modules/nf-core/diamond/cluster/tests/tags.yml b/modules/nf-core/diamond/cluster/tests/tags.yml deleted file mode 100644 index 94f299a..0000000 --- a/modules/nf-core/diamond/cluster/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -diamond/cluster: - - "modules/nf-core/diamond/cluster/**" From ef1373bc4302b171518d0ef34bd2507ce5cc128b Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 15:18:09 +0200 Subject: [PATCH 4/6] Update DIAMOND/CLUSTER again --- modules.json | 2 +- modules/nf-core/diamond/cluster/meta.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules.json b/modules.json index 5b9509e..8c7864b 100644 --- a/modules.json +++ b/modules.json @@ -22,7 +22,7 @@ }, "diamond/cluster": { "branch": "master", - "git_sha": "aecbc87790ee51c0b24fffa13aa2f34dfdd105f5", + "git_sha": "cb774ba4a9c79de334a71f802680cb66f3c8515e", "installed_by": ["modules"] }, "gawk": { diff --git a/modules/nf-core/diamond/cluster/meta.yml b/modules/nf-core/diamond/cluster/meta.yml index ee1ce1a..9c93abe 100644 --- a/modules/nf-core/diamond/cluster/meta.yml +++ b/modules/nf-core/diamond/cluster/meta.yml @@ -47,8 +47,8 @@ output: type: file description: File containing software versions pattern: "versions.yml" - ontologies: - - edam: http://edamontology.org/format_3750 # YAML + ontologies: + - edam: http://edamontology.org/format_3750 # YAML authors: - "@itrujnara" maintainers: From 04a3397ee0b56da9022a1fa564ffbee2f52f7ad9 Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 15:25:47 +0200 Subject: [PATCH 5/6] Fix nf-test config to skip testing nf-core modules --- nf-test.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf-test.config b/nf-test.config index 734122b..dbac7db 100644 --- a/nf-test.config +++ b/nf-test.config @@ -8,7 +8,7 @@ config { configFile "tests/nextflow.config" - ignore "modules/*" + ignore "modules/nf-core/**" profile "docker" From c06a94a732fc2c0cd60da785ec6146d50ed74433 Mon Sep 17 00:00:00 2001 From: itrujnara Date: Tue, 17 Jun 2025 16:52:46 +0200 Subject: [PATCH 6/6] Update test snapshot after module update --- tests/default.nf.test.snap | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index f4ae50a..99058ef 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -83,7 +83,7 @@ 245, { "DIAMOND_CLUSTER": { - "diamond": "2.1.9" + "diamond": "2.1.12" }, "DUMP_PARAMS": { "cat": 8.3 @@ -312,6 +312,6 @@ "nf-test": "0.9.2", "nextflow": "24.10.5" }, - "timestamp": "2025-06-16T15:31:06.378063481" + "timestamp": "2025-06-17T16:45:45.139534134" } } \ No newline at end of file