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Merged
merged 11 commits into from
Oct 29, 2025
Merged

Assembly subworkflow #14

merged 11 commits into from
Oct 29, 2025

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@FernandoDuarteF
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@FernandoDuarteF FernandoDuarteF commented Oct 28, 2025 •
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Closes #4.

Changes

  • Now there are two input types: --input_genome for genome submission and --input_assembly for assembly submission. Every input type has it's own samplesheet schema. --input has been removed.
  • Added validation for the two input types: one for the genome samplesheet (input_schema_genome.json) and one for the genome samplesheet (input_schema_assembly.json).

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We need a test data to start building the assembly subworkflow.

FernandoDuarteF
FernandoDuarteF commented Oct 28, 2025
View reviewed changes
subworkflows/local/utils_nfcore_seqsubmit_pipeline/main.nf
Comment on lines +99 to +107
if ( params.input_genome ) {
ch_samplesheet = Channel
.fromList(samplesheetToList(params.input_genome, "${projectDir}/assets/schema_input_genome.json"))
} else if ( params.input_assembly ) {
ch_samplesheet = Channel
.fromList(samplesheetToList(params.input_assembly, "${projectDir}/assets/schema_input_assembly.json"))
} else {
error("No input was found. Please, point to the location of your samplesheet using --input_genome or --input_assembly")
}
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@FernandoDuarteF FernandoDuarteF Oct 28, 2025 •
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This is how the validation is done now

@FernandoDuarteF
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FernandoDuarteF commented Oct 28, 2025 •
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Now there is a test for every submission type: test_genome and test_assembly. Only test_genome works (there's no assembly submission test data yet).

@FernandoDuarteF
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Added assemblysubmit.nf workflow. Now there are two workflows: assemblysubmit.nf and genomesubmit.nf. Depending on the input type one will run over the other.

assemblysubmit.nf only runs coverM for now. Test data is in assests/samplesheet_assembly.csv.

There's also a seqsubmit.nf workflow which doesn't do anything.

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Removed params.input presence check from linting (check .nf-core.yml) as it has been replaced for params.input_genome and param.input_assembly.

@FernandoDuarteF FernandoDuarteF changed the base branch from dev to assembly_workflow October 29, 2025 15:41
@FernandoDuarteF
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Pushing against nf-core:assembly_workflow (branch I've just created), as I'm pushing from my fork. If you want to still work on this you can merge it this PR and work on the nf-core:assembly_workflow branch.

@ochkalova ochkalova merged commit 222afe5 into nf-core:assembly_workflow Oct 29, 2025
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Develop nf-core subworkflow for uploading metagenomic assemblies with proper metadata handling

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@FernandoDuarteF @ochkalova