From c105c5ba10eccb1bbb6b78f162a90f0186b6b02b Mon Sep 17 00:00:00 2001 From: Ekaterina Sakharova Date: Tue, 7 Jul 2026 13:54:50 +0200 Subject: [PATCH 1/3] fixes after review --- .../create_assembly_metadata_csv/main.nf | 12 +------ .../tests/main.nf.test.snap | 34 ++++++++++--------- .../local/create_genome_metadata_tsv/main.nf | 12 +------ .../tests/main.nf.test.snap | 34 ++++++++++--------- nextflow_schema.json | 4 +-- tests/assembly_complete_metadata.nf.test.snap | 3 -- ...mbly_no_coverage_paired_reads.nf.test.snap | 3 -- ...mbly_no_coverage_single_reads.nf.test.snap | 3 -- ...ly_no_study_complete_metadata.nf.test.snap | 3 -- tests/default.nf.test.snap | 3 -- tests/mag_complete_metadata.nf.test.snap | 3 -- .../mag_no_coverage_paired_reads.nf.test.snap | 3 -- .../mag_no_coverage_single_reads.nf.test.snap | 3 -- tests/mag_no_rna_presence.nf.test.snap | 3 -- ...ag_no_study_complete_metadata.nf.test.snap | 3 -- tests/mag_no_taxonomy.nf.test.snap | 3 -- 16 files changed, 40 insertions(+), 89 deletions(-) diff --git a/modules/local/create_assembly_metadata_csv/main.nf b/modules/local/create_assembly_metadata_csv/main.nf index b7d7151..2e8283a 100644 --- a/modules/local/create_assembly_metadata_csv/main.nf +++ b/modules/local/create_assembly_metadata_csv/main.nf @@ -12,7 +12,7 @@ process CREATE_ASSEMBLY_METADATA_CSV { output: tuple val(meta), path("${meta.id}_assembly_metadata.csv"), emit: csv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bash'), eval('bash --version | head -n1 | sed "s/.*version //; s/ .*//"'), topic: versions when: task.ext.when == null || task.ext.when @@ -32,20 +32,10 @@ process CREATE_ASSEMBLY_METADATA_CSV { ${header} ${row} END_CSV - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//') - END_VERSIONS """ stub: """ touch ${meta.id}_assembly_metadata.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//') - END_VERSIONS """ } diff --git a/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap b/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap index bc1aaab..2b37721 100644 --- a/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap +++ b/modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap @@ -15,7 +15,11 @@ ] ], "1": [ - "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225" + [ + "CREATE_ASSEMBLY_METADATA_CSV", + "bash", + "5.2.37(1)-release" + ] ], "csv": [ [ @@ -28,17 +32,14 @@ }, "test_sample_assembly_metadata.csv:md5,0ad41b6b4e778fb03fc224bae9ba4529" ] - ], - "versions": [ - "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225" ] } ], + "timestamp": "2026-07-07T13:48:39.201846", "meta": { - "nf-test": "0.9.0", - "nextflow": "25.04.1" - }, - "timestamp": "2026-04-27T14:51:27.130061" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "test_create_assembly_metadata_csv - stub": { "content": [ @@ -56,7 +57,11 @@ ] ], "1": [ - "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225" + [ + "CREATE_ASSEMBLY_METADATA_CSV", + "bash", + "5.2.37(1)-release" + ] ], "csv": [ [ @@ -69,16 +74,13 @@ }, "stub_sample_assembly_metadata.csv:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "versions": [ - "versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225" ] } ], + "timestamp": "2026-07-07T13:48:46.340926", "meta": { - "nf-test": "0.9.0", - "nextflow": "25.04.1" - }, - "timestamp": "2026-04-27T14:51:32.249848" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/modules/local/create_genome_metadata_tsv/main.nf b/modules/local/create_genome_metadata_tsv/main.nf index d451f11..e78a7af 100644 --- a/modules/local/create_genome_metadata_tsv/main.nf +++ b/modules/local/create_genome_metadata_tsv/main.nf @@ -12,7 +12,7 @@ process CREATE_GENOME_METADATA_TSV { output: tuple val(meta), path("${meta.id}_genome_metadata.tsv"), emit: tsv - path "versions.yml" , emit: versions + tuple val("${task.process}"), val('bash'), eval('bash --version | head -n1 | sed "s/.*version //; s/ .*//"'), topic: versions when: task.ext.when == null || task.ext.when @@ -63,20 +63,10 @@ process CREATE_GENOME_METADATA_TSV { ${header} ${row} END_TSV - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//') - END_VERSIONS """ stub: """ touch ${meta.id}_genome_metadata.tsv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//') - END_VERSIONS """ } diff --git a/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap b/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap index 395a4e9..a073053 100644 --- a/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap +++ b/modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap @@ -26,7 +26,11 @@ ] ], "1": [ - "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a" + [ + "CREATE_GENOME_METADATA_TSV", + "bash", + "5.2.37(1)-release" + ] ], "tsv": [ [ @@ -50,17 +54,14 @@ }, "test_genome_genome_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "versions": [ - "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a" ] } ], + "timestamp": "2026-07-07T13:49:45.599115", "meta": { - "nf-test": "0.9.0", - "nextflow": "25.04.1" - }, - "timestamp": "2026-04-27T14:54:46.395718" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } }, "test_create_genome_metadata_tsv": { "content": [ @@ -89,7 +90,11 @@ ] ], "1": [ - "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a" + [ + "CREATE_GENOME_METADATA_TSV", + "bash", + "5.2.37(1)-release" + ] ], "tsv": [ [ @@ -113,16 +118,13 @@ }, "test_genome_genome_metadata.tsv:md5,64562a85d19fe5893cad0e89e894058a" ] - ], - "versions": [ - "versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a" ] } ], + "timestamp": "2026-07-07T13:49:37.674712", "meta": { - "nf-test": "0.9.0", - "nextflow": "25.04.1" - }, - "timestamp": "2026-04-27T14:54:41.692391" + "nf-test": "0.9.5", + "nextflow": "26.04.0" + } } } \ No newline at end of file diff --git a/nextflow_schema.json b/nextflow_schema.json index 1f628b6..59c6dc0 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/master/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/seqsubmit/main/nextflow_schema.json", "title": "nf-core/seqsubmit pipeline parameters", "description": "Submit sequences, assemblies, MAGs, etc., to public archives", "type": "object", @@ -17,7 +17,7 @@ "format": "file-path", "exists": true, "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", + "pattern": "^\\S+\\.(csv|tsv|yaml|yml|json)$", "description": "Path to comma-separated file describing the data to be submitted. Format depends on the pipeline mode (mags/bins/metagenomic_assemblies/reads).", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a set of columns depending on the type of data being submitted. See [usage docs](https://nf-co.re/seqsubmit/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" diff --git a/tests/assembly_complete_metadata.nf.test.snap b/tests/assembly_complete_metadata.nf.test.snap index 2793fd6..f0c8e34 100644 --- a/tests/assembly_complete_metadata.nf.test.snap +++ b/tests/assembly_complete_metadata.nf.test.snap @@ -13,9 +13,6 @@ "find": "4.6.0", "pigz": 2.8 }, - "CREATE_ASSEMBLY_METADATA_CSV": { - "bash": "5.2.37(1)-release" - }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_coverage_paired_reads.nf.test.snap b/tests/assembly_no_coverage_paired_reads.nf.test.snap index 533388e..c6bd576 100644 --- a/tests/assembly_no_coverage_paired_reads.nf.test.snap +++ b/tests/assembly_no_coverage_paired_reads.nf.test.snap @@ -16,9 +16,6 @@ "COVERM_CONTIG": { "coverm": "0.7.0" }, - "CREATE_ASSEMBLY_METADATA_CSV": { - "bash": "5.2.37(1)-release" - }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_coverage_single_reads.nf.test.snap b/tests/assembly_no_coverage_single_reads.nf.test.snap index 67ccc9b..fc5f241 100644 --- a/tests/assembly_no_coverage_single_reads.nf.test.snap +++ b/tests/assembly_no_coverage_single_reads.nf.test.snap @@ -16,9 +16,6 @@ "COVERM_CONTIG": { "coverm": "0.7.0" }, - "CREATE_ASSEMBLY_METADATA_CSV": { - "bash": "5.2.37(1)-release" - }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_study_complete_metadata.nf.test.snap b/tests/assembly_no_study_complete_metadata.nf.test.snap index a834d6d..680e3d1 100644 --- a/tests/assembly_no_study_complete_metadata.nf.test.snap +++ b/tests/assembly_no_study_complete_metadata.nf.test.snap @@ -13,9 +13,6 @@ "find": "4.6.0", "pigz": 2.8 }, - "CREATE_ASSEMBLY_METADATA_CSV": { - "bash": "5.2.37(1)-release" - }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 9968b79..4dee107 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -31,9 +31,6 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap index 7c7f539..d182715 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -13,9 +13,6 @@ "find": "4.6.0", "pigz": 2.8 }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_coverage_paired_reads.nf.test.snap b/tests/mag_no_coverage_paired_reads.nf.test.snap index 894e756..112eb23 100644 --- a/tests/mag_no_coverage_paired_reads.nf.test.snap +++ b/tests/mag_no_coverage_paired_reads.nf.test.snap @@ -16,9 +16,6 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_coverage_single_reads.nf.test.snap b/tests/mag_no_coverage_single_reads.nf.test.snap index 767748f..daf7265 100644 --- a/tests/mag_no_coverage_single_reads.nf.test.snap +++ b/tests/mag_no_coverage_single_reads.nf.test.snap @@ -16,9 +16,6 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_rna_presence.nf.test.snap b/tests/mag_no_rna_presence.nf.test.snap index 8a7d21c..27b72e9 100644 --- a/tests/mag_no_rna_presence.nf.test.snap +++ b/tests/mag_no_rna_presence.nf.test.snap @@ -19,9 +19,6 @@ "COUNT_RNA": { "python": "3.12.12" }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_study_complete_metadata.nf.test.snap b/tests/mag_no_study_complete_metadata.nf.test.snap index 1aea1e8..61c0b5a 100644 --- a/tests/mag_no_study_complete_metadata.nf.test.snap +++ b/tests/mag_no_study_complete_metadata.nf.test.snap @@ -13,9 +13,6 @@ "find": "4.6.0", "pigz": 2.8 }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_taxonomy.nf.test.snap b/tests/mag_no_taxonomy.nf.test.snap index 1563d4b..22c1d7b 100644 --- a/tests/mag_no_taxonomy.nf.test.snap +++ b/tests/mag_no_taxonomy.nf.test.snap @@ -22,9 +22,6 @@ "find": "4.6.0", "pigz": 2.8 }, - "CREATE_GENOME_METADATA_TSV": { - "bash": "5.2.37(1)-release" - }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, From ae4a2f4610d41465fa36a3a56a75f83d2f8ed936 Mon Sep 17 00:00:00 2001 From: Ekaterina Sakharova Date: Tue, 7 Jul 2026 16:01:39 +0200 Subject: [PATCH 2/3] fix --- workflows/assemblysubmit.nf | 1 - workflows/genomesubmit.nf | 1 - 2 files changed, 2 deletions(-) diff --git a/workflows/assemblysubmit.nf b/workflows/assemblysubmit.nf index 2acf2b1..84a9dc8 100644 --- a/workflows/assemblysubmit.nf +++ b/workflows/assemblysubmit.nf @@ -139,7 +139,6 @@ workflow ASSEMBLYSUBMIT { CREATE_ASSEMBLY_METADATA_CSV( assemblies_with_coverage ) - ch_versions = ch_versions.mix(CREATE_ASSEMBLY_METADATA_CSV.out.versions) // Concatenate assembly metadata CSVs into single file to publish CONCAT_METADATA ( diff --git a/workflows/genomesubmit.nf b/workflows/genomesubmit.nf index 18edd96..8c1df8e 100644 --- a/workflows/genomesubmit.nf +++ b/workflows/genomesubmit.nf @@ -252,7 +252,6 @@ workflow GENOMESUBMIT { CREATE_GENOME_METADATA_TSV ( fasta_updated_with_taxonomy ) - ch_versions = ch_versions.mix(CREATE_GENOME_METADATA_TSV.out.versions) // Collect all TSV rows into a single file CONCAT_METADATA ( From 1f62e1e5c01dd46565adbb0075bbdee92ac34d8f Mon Sep 17 00:00:00 2001 From: Ekaterina Sakharova Date: Tue, 7 Jul 2026 16:13:13 +0200 Subject: [PATCH 3/3] fix --- tests/assembly_complete_metadata.nf.test.snap | 3 +++ tests/assembly_no_coverage_paired_reads.nf.test.snap | 3 +++ tests/assembly_no_coverage_single_reads.nf.test.snap | 3 +++ tests/assembly_no_study_complete_metadata.nf.test.snap | 3 +++ tests/default.nf.test.snap | 3 +++ tests/mag_complete_metadata.nf.test.snap | 3 +++ tests/mag_no_coverage_paired_reads.nf.test.snap | 3 +++ tests/mag_no_coverage_single_reads.nf.test.snap | 3 +++ tests/mag_no_rna_presence.nf.test.snap | 3 +++ tests/mag_no_study_complete_metadata.nf.test.snap | 3 +++ tests/mag_no_taxonomy.nf.test.snap | 3 +++ 11 files changed, 33 insertions(+) diff --git a/tests/assembly_complete_metadata.nf.test.snap b/tests/assembly_complete_metadata.nf.test.snap index f0c8e34..2793fd6 100644 --- a/tests/assembly_complete_metadata.nf.test.snap +++ b/tests/assembly_complete_metadata.nf.test.snap @@ -13,6 +13,9 @@ "find": "4.6.0", "pigz": 2.8 }, + "CREATE_ASSEMBLY_METADATA_CSV": { + "bash": "5.2.37(1)-release" + }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_coverage_paired_reads.nf.test.snap b/tests/assembly_no_coverage_paired_reads.nf.test.snap index c6bd576..533388e 100644 --- a/tests/assembly_no_coverage_paired_reads.nf.test.snap +++ b/tests/assembly_no_coverage_paired_reads.nf.test.snap @@ -16,6 +16,9 @@ "COVERM_CONTIG": { "coverm": "0.7.0" }, + "CREATE_ASSEMBLY_METADATA_CSV": { + "bash": "5.2.37(1)-release" + }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_coverage_single_reads.nf.test.snap b/tests/assembly_no_coverage_single_reads.nf.test.snap index fc5f241..67ccc9b 100644 --- a/tests/assembly_no_coverage_single_reads.nf.test.snap +++ b/tests/assembly_no_coverage_single_reads.nf.test.snap @@ -16,6 +16,9 @@ "COVERM_CONTIG": { "coverm": "0.7.0" }, + "CREATE_ASSEMBLY_METADATA_CSV": { + "bash": "5.2.37(1)-release" + }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/assembly_no_study_complete_metadata.nf.test.snap b/tests/assembly_no_study_complete_metadata.nf.test.snap index 680e3d1..a834d6d 100644 --- a/tests/assembly_no_study_complete_metadata.nf.test.snap +++ b/tests/assembly_no_study_complete_metadata.nf.test.snap @@ -13,6 +13,9 @@ "find": "4.6.0", "pigz": 2.8 }, + "CREATE_ASSEMBLY_METADATA_CSV": { + "bash": "5.2.37(1)-release" + }, "FALINT": { "falint": "1.2.0" }, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4dee107..9968b79 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -31,6 +31,9 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_complete_metadata.nf.test.snap b/tests/mag_complete_metadata.nf.test.snap index d182715..7c7f539 100644 --- a/tests/mag_complete_metadata.nf.test.snap +++ b/tests/mag_complete_metadata.nf.test.snap @@ -13,6 +13,9 @@ "find": "4.6.0", "pigz": 2.8 }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_coverage_paired_reads.nf.test.snap b/tests/mag_no_coverage_paired_reads.nf.test.snap index 112eb23..894e756 100644 --- a/tests/mag_no_coverage_paired_reads.nf.test.snap +++ b/tests/mag_no_coverage_paired_reads.nf.test.snap @@ -16,6 +16,9 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_coverage_single_reads.nf.test.snap b/tests/mag_no_coverage_single_reads.nf.test.snap index daf7265..767748f 100644 --- a/tests/mag_no_coverage_single_reads.nf.test.snap +++ b/tests/mag_no_coverage_single_reads.nf.test.snap @@ -16,6 +16,9 @@ "COVERM_GENOME": { "coverm": "0.7.0" }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_rna_presence.nf.test.snap b/tests/mag_no_rna_presence.nf.test.snap index 27b72e9..8a7d21c 100644 --- a/tests/mag_no_rna_presence.nf.test.snap +++ b/tests/mag_no_rna_presence.nf.test.snap @@ -19,6 +19,9 @@ "COUNT_RNA": { "python": "3.12.12" }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_study_complete_metadata.nf.test.snap b/tests/mag_no_study_complete_metadata.nf.test.snap index 61c0b5a..1aea1e8 100644 --- a/tests/mag_no_study_complete_metadata.nf.test.snap +++ b/tests/mag_no_study_complete_metadata.nf.test.snap @@ -13,6 +13,9 @@ "find": "4.6.0", "pigz": 2.8 }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" }, diff --git a/tests/mag_no_taxonomy.nf.test.snap b/tests/mag_no_taxonomy.nf.test.snap index 22c1d7b..1563d4b 100644 --- a/tests/mag_no_taxonomy.nf.test.snap +++ b/tests/mag_no_taxonomy.nf.test.snap @@ -22,6 +22,9 @@ "find": "4.6.0", "pigz": 2.8 }, + "CREATE_GENOME_METADATA_TSV": { + "bash": "5.2.37(1)-release" + }, "CREATE_MANIFESTS": { "genome_uploader": "3.0.1" },