From 7971b4516489cf2df030c01ae02dba026c04ab02 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 11 Dec 2024 09:44:21 +0100 Subject: [PATCH 1/3] Make eukulele count files optional --- modules/local/eukulele/search.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/local/eukulele/search.nf b/modules/local/eukulele/search.nf index b9677220..e3cc9126 100644 --- a/modules/local/eukulele/search.nf +++ b/modules/local/eukulele/search.nf @@ -12,7 +12,7 @@ process EUKULELE_SEARCH { output: tuple val(meta), path("*/taxonomy_estimation/*.out.gz"), val("${dbname}") , emit: taxonomy_estimation - tuple val(meta), path("*/taxonomy_counts/*.csv.gz") , emit: taxonomy_counts + tuple val(meta), path("*/taxonomy_counts/*.csv.gz") , emit: taxonomy_counts , optional: true tuple val(meta), path("*/mets_full/diamond/*") , emit: diamond path "versions.yml" , emit: versions @@ -38,7 +38,7 @@ process EUKULELE_SEARCH { contigs || rc=\$? gzip ${prefix}/mets_full/diamond/*.out - gzip ${prefix}/taxonomy_counts/*.csv + find ${prefix}/taxonomy_counts/ -name "*.csv" | xargs gzip gzip ${prefix}/taxonomy_estimation/*.out cat <<-END_VERSIONS > versions.yml From 173afecfcc6926287cf2a0ab21932f77a78c8f84 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 11 Dec 2024 09:53:14 +0100 Subject: [PATCH 2/3] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index dcd4858a..81a7584c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ Initial release of nf-core/metatdenovo, created with the [nf-core](https://nf-co ### `Fixed` +- [#304](<[https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/304)>) - Make EUKulele counts output optional as it's not always created - [#269](<[https://github.com/nf-core/ampliseq/pull/681](https://github.com/nf-core/metatdenovo/pull/269)>) - Make Transdecoder work better with `-resume` ### `Dependencies` From dff8dc9dc0d5f70bf609431b7e5325b50a5576a9 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Wed, 11 Dec 2024 09:57:05 +0100 Subject: [PATCH 3/3] Fix schema urls --- assets/schema_input.json | 2 +- nextflow_schema.json | 2 +- .../utils_nfvalidation_plugin/tests/nextflow_schema.json | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index 8ebba037..ed41bab9 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/metatdenovo/master/assets/schema_input.json", "title": "nf-core/metatdenovo pipeline - params.input schema", "description": "Schema for the file provided with params.input", diff --git a/nextflow_schema.json b/nextflow_schema.json index 5d623cca..bf85c5ba 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/metatdenovo/master/nextflow_schema.json", "title": "nf-core/metatdenovo pipeline parameters", "description": "Assembly and annotation of metatranscriptomic data, both prokaryotic and eukaryotic", diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json index 7626c1c9..b7af0b57 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/nextflow_schema.json @@ -1,5 +1,5 @@ { - "$schema": "http://json-schema.org/draft-07/schema", + "$schema": "https://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "title": ". pipeline parameters", "description": "",