diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf b/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf index 937fbec7b205..3723cb74905f 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/main.nf @@ -159,14 +159,14 @@ workflow FASTA_GXF_BUSCO_PLOT { assembly_batch_summary = ch_assembly_batch_summary // channel: [ meta3, txt ]; meta3 ~ meta + [ val(mode), val(lineage) ] assembly_short_summaries_txt = ch_assembly_short_summaries_txt // channel: [ meta3, txt ] assembly_short_summaries_json = ch_assembly_short_summaries_json // channel: [ meta3, json ] + assembly_full_table = ch_assembly_full_table // channel: [ meta3, tsv ] assembly_plot_summary_txt = ch_assembly_plot_summary // channel: [ text ] - assembly_full_table = ch_assembly_full_table // channel: [ meta3, tsv ] assembly_png = ch_assembly_png // channel: [ png ] annotation_batch_summary = ch_annotation_batch_summary // channel: [ meta3, txt ] annotation_short_summaries_txt = ch_annotation_short_summaries_txt // channel: [ meta3, txt ] annotation_short_summaries_json = ch_annotation_short_summaries_json // channel: [ meta3, json ] + annotation_full_table = ch_annotation_full_table // channel: [ meta3, tsv ] annotation_plot_summary_txt = ch_annotation_plot_summary // channel: [ txt ] - annotation_full_table = ch_annotation_full_table // channel: [ meta3, tsv ] annotation_png = ch_annotation_png // channel: [ png ] versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml b/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml index 6ae8afec7620..bf0e437f326b 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/meta.yml @@ -64,6 +64,12 @@ output: Channel containing BUSCO short summaries corresponding to fasta files Structure: [ val(meta), json ] pattern: "*.json" + - assembly_full_table: + description: | + Channel containing complete results in a tabular format with scores and lengths of BUSCO matches, + and coordinates (for genome mode) or gene/protein IDs (for transcriptome or protein modes) + Structure: [ val(meta), tsv ] + pattern: "*.tsv" - assembly_plot_summary_txt: type: file description: | @@ -94,6 +100,12 @@ output: Channel containing BUSCO short summaries corresponding to annotation files Structure: [ val(meta), json ] pattern: "*.json" + - annotation_full_table: + description: | + Channel containing complete results in a tabular format with scores and lengths of BUSCO matches, + protein IDs in protein mode + Structure: [ val(meta), tsv ] + pattern: "*.tsv" - annotation_plot_summary_txt: type: file description: | @@ -116,3 +128,4 @@ authors: - "@GallVp" maintainers: - "@GallVp" + - "@FernandoDuarteF" diff --git a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap index 44a8c99dda1c..89604dc25c03 100644 --- a/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fasta_gxf_busco_plot/tests/main.nf.test.snap @@ -40,6 +40,12 @@ ], "10": [ + + ], + "11": [ + + ], + "12": [ "versions.yml:md5,36b11c442943567e471af0abd474a10b", "versions.yml:md5,9435355f913e283f60b4fb7ef77dd52a", "versions.yml:md5,e9d65e2f2f13175e99c5b7f4ae1013b9" @@ -54,6 +60,9 @@ ], "5": [ + + ], + "6": [ [ { "id": "test", @@ -70,9 +79,6 @@ }, "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "6": [ - ], "7": [ @@ -100,6 +106,9 @@ }, "test-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "annotation_full_table": [ + ], "annotation_plot_summary_txt": [ @@ -146,6 +155,9 @@ }, "test2-bacteria_odb10-busco.batch_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "assembly_full_table": [ + ], "assembly_plot_summary_txt": [ @@ -168,9 +180,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.1" }, - "timestamp": "2024-11-20T14:04:28.17169" + "timestamp": "2024-11-25T10:31:03.980517" }, "candidatus_portiera_aleyrodidarum - bacteroides_fragilis - genome": { "content": [