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Merged
KateSakharova merged 3 commits into from
Jul 7, 2026
Merged

fixes after review #82

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c105c5b
fixes after review
KateSakharova Jul 7, 2026
ae4a2f4
fix
KateSakharova Jul 7, 2026
1f62e1e
fix
KateSakharova Jul 7, 2026
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12 changes: 1 addition & 11 deletions modules/local/create_assembly_metadata_csv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
"""
}
34 changes: 18 additions & 16 deletions modules/local/create_assembly_metadata_csv/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,11 @@
]
],
"1": [
"versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
[
"CREATE_ASSEMBLY_METADATA_CSV",
"bash",
"5.2.37(1)-release"
]
],
"csv": [
[
Expand All @@ -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": [
Expand All @@ -56,7 +57,11 @@
]
],
"1": [
"versions.yml:md5,1dbd8a6b5ae469b5f51d5c96b7ab3225"
[
"CREATE_ASSEMBLY_METADATA_CSV",
"bash",
"5.2.37(1)-release"
]
],
"csv": [
[
Expand All @@ -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"
}
}
}
12 changes: 1 addition & 11 deletions modules/local/create_genome_metadata_tsv/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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
"${task.process}":
bash: \$(bash --version | head -n1 | sed 's/.*version //; s/ .*//')
END_VERSIONS
"""
}
34 changes: 18 additions & 16 deletions modules/local/create_genome_metadata_tsv/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,11 @@
]
],
"1": [
"versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
[
"CREATE_GENOME_METADATA_TSV",
"bash",
"5.2.37(1)-release"
]
],
"tsv": [
[
Expand All @@ -50,17 +54,14 @@
},
"test_genome_genome_metadata.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
]
}
],
"timestamp": "2026-07-07T13:49:45.599115",
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.1"
},
"timestamp": "2026-04-27T14:54:46.395718"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"test_create_genome_metadata_tsv": {
"content": [
Expand Down Expand Up @@ -89,7 +90,11 @@
]
],
"1": [
"versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
[
"CREATE_GENOME_METADATA_TSV",
"bash",
"5.2.37(1)-release"
]
],
"tsv": [
[
Expand All @@ -113,16 +118,13 @@
},
"test_genome_genome_metadata.tsv:md5,64562a85d19fe5893cad0e89e894058a"
]
],
"versions": [
"versions.yml:md5,aa5a1803455c1cb3200667da8c471d6a"
]
}
],
"timestamp": "2026-07-07T13:49:37.674712",
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.1"
},
"timestamp": "2026-04-27T14:54:41.692391"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
4 changes: 2 additions & 2 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
{
"$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",
Expand All @@ -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"
Expand Down
1 change: 0 additions & 1 deletion workflows/assemblysubmit.nf
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Expand Up @@ -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 (
Expand Down
1 change: 0 additions & 1 deletion workflows/genomesubmit.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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 (
Expand Down
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