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Fix io of resfinder for all workflows but saureus #408

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merged 2 commits into from
Feb 20, 2025
Merged

Fix io of resfinder for all workflows but saureus #408

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92b2251
Fix io of resfinder for all workflows but saureus
ryanjameskennedy Feb 20, 2025
b6d2a3d
Update CHANGELOG re io fix for postalignqc and resfinder
ryanjameskennedy Feb 20, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -51,6 +51,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Fixed sccmec version file
- Fixed handling of ONT samples re fastqc & postalignqc
- Fixed io of spatyper and turned on postalignqc for ONT
- Fixed io of resfinder for all workflows but saureus
- Fixed input array for postalignqc

### Changed

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2 changes: 1 addition & 1 deletion nextflow-modules/modules/prp/main.nf
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Expand Up @@ -117,7 +117,7 @@ process post_align_qc {
scratch params.scratch

input:
tuple val(sample_id), path(bam), val(platform)
tuple val(sample_id), path(bam)
path reference
path bed

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2 changes: 1 addition & 1 deletion workflows/bacterial_base.nf
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Expand Up @@ -101,7 +101,7 @@ workflow CALL_BACTERIAL_BASE {
bwa_mem_ref(ch_reads, referenceGenomeDir)
samtools_index_ref(bwa_mem_ref.out.bam)

post_align_qc(bwa_mem_ref.out.bam.join(ch_meta), referenceGenome, coreLociBed)
post_align_qc(bwa_mem_ref.out.bam, referenceGenome, coreLociBed)

nanoplot(ch_reads_w_meta)

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2 changes: 1 addition & 1 deletion workflows/escherichia_coli.nf
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Expand Up @@ -114,7 +114,7 @@ workflow CALL_ESCHERICHIA_COLI {
amrfinderplus(ch_assembly, params.species, amrfinderDb)

// resistance & virulence prediction
resfinder(ch_reads, params.species, resfinderDb, pointfinderDb)
resfinder(ch_input_meta, params.species, resfinderDb, pointfinderDb)
virulencefinder(ch_reads, params.useVirulenceDbs, virulencefinderDb)

ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
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2 changes: 1 addition & 1 deletion workflows/klebsiella_pneumoniae.nf
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Expand Up @@ -111,7 +111,7 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {
amrfinderplus(ch_assembly, params.species, amrfinderDb)

// resistance & virulence prediction
resfinder(ch_reads, params.species, resfinderDb, pointfinderDb)
resfinder(ch_input_meta, params.species, resfinderDb, pointfinderDb)
virulencefinder(ch_reads, params.useVirulenceDbs, virulencefinderDb)

ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
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2 changes: 1 addition & 1 deletion workflows/streptococcus.nf
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Expand Up @@ -122,7 +122,7 @@ workflow CALL_STREPTOCOCCUS {
amrfinderplus(ch_assembly, species, amrfinderDb)

// resistance & virulence prediction
resfinder(ch_reads, species, resfinderDb, pointfinderDb)
resfinder(ch_input_meta, species, resfinderDb, pointfinderDb)
virulencefinder(ch_reads, params.useVirulenceDbs, virulencefinderDb)

ch_reads.map{ sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
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2 changes: 1 addition & 1 deletion workflows/streptococcus_pyogenes.nf
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Expand Up @@ -114,7 +114,7 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
amrfinderplus(ch_assembly, params.species, amrfinderDb)

// resistance & virulence prediction
resfinder(ch_reads, params.species, resfinderDb, pointfinderDb)
resfinder(ch_input_meta, params.species, resfinderDb, pointfinderDb)
virulencefinder(ch_reads, params.useVirulenceDbs, virulencefinderDb)

ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
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