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Add single copy sequence file output to busco/busco #7779

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Add single copy sequence file output to busco/busco #7779

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26 changes: 14 additions & 12 deletions modules/nf-core/busco/busco/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,19 +16,21 @@ process BUSCO_BUSCO {
val clean_intermediates // Optional: Remove intermediate files

output:
tuple val(meta), path("*-busco.batch_summary.txt") , emit: batch_summary
tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt , optional: true
tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json , optional: true
tuple val(meta), path("*-busco/logs/busco.log") , emit: log , optional: true
tuple val(meta), path("*-busco/*/run_*/full_table.tsv") , emit: full_table , optional: true
tuple val(meta), path("*-busco/*/run_*/missing_busco_list.tsv") , emit: missing_busco_list , optional: true
tuple val(meta), path("*-busco/*/run_*/single_copy_proteins.faa") , emit: single_copy_proteins , optional: true
tuple val(meta), path("*-busco/*/run_*/busco_sequences") , emit: seq_dir , optional: true
tuple val(meta), path("*-busco/*/translated_proteins") , emit: translated_dir , optional: true
tuple val(meta), path("*-busco") , emit: busco_dir
tuple val(meta), path("busco_downloads/lineages/*") , emit: downloaded_lineages , optional: true
tuple val(meta), path("*-busco.batch_summary.txt") , emit: batch_summary
tuple val(meta), path("short_summary.*.txt") , emit: short_summaries_txt , optional: true
tuple val(meta), path("short_summary.*.json") , emit: short_summaries_json , optional: true
tuple val(meta), path("*-busco/logs/busco.log") , emit: log , optional: true
tuple val(meta), path("*-busco/*/run_*/full_table.tsv") , emit: full_table , optional: true
tuple val(meta), path("*-busco/*/run_*/missing_busco_list.tsv") , emit: missing_busco_list , optional: true
tuple val(meta), path("*-busco/*/run_*/single_copy_proteins.faa") , emit: single_copy_proteins , optional: true
tuple val(meta), path("*-busco/*/run_*/busco_sequences") , emit: seq_dir , optional: true
tuple val(meta), path("*-busco/*/translated_proteins") , emit: translated_dir , optional: true
tuple val(meta), path("*-busco") , emit: busco_dir
tuple val(meta), path("busco_downloads/lineages/*") , emit: downloaded_lineages , optional: true
tuple val(meta), path("*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa"), emit: single_copy_faa , optional: true
tuple val(meta), path("*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna"), emit: single_copy_fna , optional: true

path "versions.yml" , emit: versions
path "versions.yml" , emit: versions

when:
task.ext.when == null || task.ext.when
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20 changes: 20 additions & 0 deletions modules/nf-core/busco/busco/meta.yml
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Expand Up @@ -155,6 +155,26 @@ output:
type: directory
description: Lineages downloaded by BUSCO when running the analysis, for example bacteria_odb12
pattern: "busco_downloads/lineages/*"
- single_copy_faa:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa":
type: file
description: Single copy .faa sequence files
pattern: "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.faa"
- single_copy_fna:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test' ]
- "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna":
type: file
description: Single copy .fna sequence files
pattern: "*-busco/*/run_*/busco_sequences/single_copy_busco_sequences/*.fna"
- versions:
- versions.yml:
type: file
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2 changes: 1 addition & 1 deletion modules/nf-core/busco/busco/tests/main.nf.test
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Expand Up @@ -425,7 +425,7 @@ nextflow_process {
assert contains('Results from dataset')
assert contains('how to cite BUSCO')
}

assert path("${process.out.busco_dir[0][1]}/*/auto_lineage").exists() == false
assert path("${process.out.busco_dir[0][1]}/*/**/{miniprot,hmmer,.bbtools}_output").exists() == false

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4 changes: 2 additions & 2 deletions modules/nf-core/busco/phylogenomics/tests/main.nf.test
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Expand Up @@ -57,7 +57,7 @@ nextflow_process {
).match()
},
{ assert new File(geneTreeDir, geneTreeDir.list().find { file(it).name == "ALL.tree" }).exists() },
{ assert new File(supermatrixDir, supermatrixDir.list().find { file(it).name == "SUPERMATRIX.fasta" }).text.contains("MTDPIADYLTRLRNAINAKHRVVEVPASNLKKEITKILFEKGYILNYKFVEDGPQGTIKV") },
{ assert new File(supermatrixDir, supermatrixDir.list().find { file(it).name == "SUPERMATRIX.fasta" }).text.contains("MPGLLGKKIGMTSVFSADGKNVPCTVIEAGPCVVTQVKTVEKDGYAAVQLGFQDKKEKHT") },
{ assert new File(supermatrixDir, supermatrixDir.list().find { file(it).name == "SUPERMATRIX.partitions.nex" }).text.contains("#nexus\nbegin sets;\n\tcharset") },
{ assert new File(supermatrixDir, supermatrixDir.list().find { file(it).name == "SUPERMATRIX.phylip" }).text.contains(" 1 36572\ngenome.fna") }
)
Expand Down Expand Up @@ -86,4 +86,4 @@ nextflow_process {

}

}
}
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