Fix io of resfinder for all workflows but saureus

genomic-medicine-sweden · Feb 20, 2025 · 92b2251 · 92b2251
1 parent 3ca1064
commit 92b2251
Show file tree

Hide file tree

Showing 7 changed files with 7 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -51,6 +51,7 @@ 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
 
 ### Changed
 

diff --git a/nextflow-modules/modules/prp/main.nf b/nextflow-modules/modules/prp/main.nf
@@ -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
 

diff --git a/workflows/bacterial_base.nf b/workflows/bacterial_base.nf
@@ -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)
 

diff --git a/workflows/escherichia_coli.nf b/workflows/escherichia_coli.nf
@@ -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 }

diff --git a/workflows/klebsiella_pneumoniae.nf b/workflows/klebsiella_pneumoniae.nf
@@ -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 }

diff --git a/workflows/streptococcus.nf b/workflows/streptococcus.nf
@@ -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 }

diff --git a/workflows/streptococcus_pyogenes.nf b/workflows/streptococcus_pyogenes.nf
@@ -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 }