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fix: Avoid file location issue with ppanggolin/poppunk #193

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merged 4 commits into from
May 11, 2024
Merged

fix: Avoid file location issue with ppanggolin/poppunk #193

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b14ca29
refactor: Add assemblies to poppunk process input
jvfe May 9, 2024
f1c93b6
refactor: Add gffs to ppanggolin/panaroo input
jvfe May 9, 2024
95c5489
Merge remote-tracking branch 'origin/master' into fix-samplesheets
jvfe May 10, 2024
a2b0c79
tests: Add file to files in nf-tests
jvfe May 11, 2024
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1 change: 1 addition & 0 deletions modules/local/poppunk/createdb/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ process POPPUNK_CREATEDB {
input:

path filesheet
path assemblies

output:

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1 change: 1 addition & 0 deletions modules/local/ppanggolin/workflow/main.nf
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Expand Up @@ -11,6 +11,7 @@ process PPANGGOLIN_WORKFLOW {

input:
tuple val(meta), path(samplesheet)
path gffs

output:
tuple val(meta), path("$prefix") , emit: results
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1 change: 1 addition & 0 deletions modules/nf-core/panaroo/run/main.nf
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Expand Up @@ -9,6 +9,7 @@ process PANAROO_RUN {

input:
tuple val(meta), path(gff)
path gffs

output:
tuple val(meta), path("results/*") , emit: results
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6 changes: 3 additions & 3 deletions subworkflows/local/phylo.nf
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Expand Up @@ -26,7 +26,7 @@ workflow PHYLOGENOMICS{
ch_software_versions = Channel.empty()

gffs
.map { meta, path -> [meta.id, path.toString()] }
.map { meta, path -> [meta.id, path.getName()] }
.set { gff_paths }

// Create samplesheet
Expand All @@ -39,7 +39,7 @@ workflow PHYLOGENOMICS{
.map{ path -> [[id: 'ppanggolin'], path] }
.set { gff_samplesheet }

PPANGGOLIN_WORKFLOW(gff_samplesheet)
PPANGGOLIN_WORKFLOW(gff_samplesheet, gffs.collect{ it[1] })

PPANGGOLIN_WORKFLOW.out.pangenome.set { pangenome }

Expand Down Expand Up @@ -76,7 +76,7 @@ workflow PHYLOGENOMICS{
* Core gene identification and alignment
*/
// By default, run panaroo
PANAROO_RUN(gff_samplesheet)
PANAROO_RUN(gff_samplesheet, gffs.collect{ it[1] })
PANAROO_RUN.out.aln.collect{ meta, aln -> aln }.set{ ch_core_alignment }
PANAROO_RUN.out.accessory_aln.set{ ch_all_alignments }

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4 changes: 2 additions & 2 deletions subworkflows/local/poppunk.nf
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Expand Up @@ -24,14 +24,14 @@ workflow RUN_POPPUNK {
}

genome_assemblies
.map { meta, path -> [meta.id, path.toString()] }
.map { meta, path -> [meta.id, path.getName()] }
.collectFile(newLine: true) { item ->
[ "${item[0]}.txt", item[0] + '\t' + item[1] ]
}
.collectFile(name: 'poppunk_samplesheet.tsv')
.set { poppunk_samplesheet }

POPPUNK_CREATEDB(poppunk_samplesheet)
POPPUNK_CREATEDB(poppunk_samplesheet, genome_assemblies.collect { it[1] } )

POPPUNK_CREATEDB.out.poppunk_db.set { poppunk_db }

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6 changes: 3 additions & 3 deletions tests/subworkflows/local/phylo.nf.test
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Expand Up @@ -15,9 +15,9 @@ nextflow_workflow {
"""
// define inputs of the workflow here. Example:
input[0] = Channel.of(
[[id:'SRR14022735'], '$baseDir/test/SRR14022735_T1.gff'],
[[id:'SRR14022764'], '$baseDir/test/SRR14022764_T1.gff'],
[[id:'SRR14022754'], '$baseDir/test/SRR14022754_T1.gff']
[[id:'SRR14022735'], file('$baseDir/test/SRR14022735_T1.gff')],
[[id:'SRR14022764'], file('$baseDir/test/SRR14022764_T1.gff')],
[[id:'SRR14022754'], file('$baseDir/test/SRR14022754_T1.gff')]
)
// Don't use full alignment
input[1] = false
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8 changes: 4 additions & 4 deletions tests/subworkflows/local/poppunk.nf.test.skip
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Expand Up @@ -15,10 +15,10 @@ nextflow_workflow {
"""
// define inputs of the workflow here. Example:
input[0] = Channel.of(
[[id:'SRR14022735'], "$baseDir/test/SRR14022735_T1.scaffolds.fa"],
[[id:'SRR14022737'], "$baseDir/test/SRR14022737_T1.scaffolds.fa"],
[[id:'SRR14022754'], "$baseDir/test/SRR14022754_T1.scaffolds.fa"],
[[id:'SRR14022764'], "$baseDir/test/SRR14022764_T1.scaffolds.fa"],
[[id:'SRR14022735'], file("$baseDir/test/SRR14022735_T1.scaffolds.fa")],
[[id:'SRR14022737'], file("$baseDir/test/SRR14022737_T1.scaffolds.fa")],
[[id:'SRR14022754'], file("$baseDir/test/SRR14022754_T1.scaffolds.fa")],
[[id:'SRR14022764'], file("$baseDir/test/SRR14022764_T1.scaffolds.fa")],
)
"""
}
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