Fixes to hopper config and saureus workflow

genomic-medicine-sweden · Oct 25, 2024 · 425bb85 · 425bb85
1 parent a4b71d4
commit 425bb85
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Showing 4 changed files with 10 additions and 24 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -25,6 +25,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Empty channels fixed
 - Chewbbaca collection of input fixed
 - Fixed resfinder `--species` arg
+- Fixed `nextflow.hopper.config` `symlinkDir`
+- Removed serotypefinder from saureus workflow
 
 ### Changed
 

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -77,7 +77,7 @@ profiles {
 		params.species = 'klebsiella pneumoniae'
 		params.speciesDir = 'kpneumoniae'
 		params.mlstScheme = 'klebsiella'
-		params.symlinkDir = "/access/jasen/kpneumoniae/
+		params.symlinkDir = "/access/jasen/kpneumoniae/"
 		params.referenceGenome = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff"
@@ -93,7 +93,7 @@ profiles {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
 		params.resistantLociName = 'resistance_loci'
-		params.symlinkDir = "/access/jasen/mtuberculosis/
+		params.symlinkDir = "/access/jasen/mtuberculosis/"
 		params.referenceGenome = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"

diff --git a/workflows/staphylococcus_aureus.nf b/workflows/staphylococcus_aureus.nf
@@ -21,7 +21,6 @@ include { mask_polymorph_assembly                   } from '../nextflow-modules/
 include { mlst                                      } from '../nextflow-modules/modules/mlst/main.nf'
 include { resfinder                                 } from '../nextflow-modules/modules/resfinder/main.nf'
 include { samtools_index as samtools_index_assembly } from '../nextflow-modules/modules/samtools/main.nf'
-include { serotypefinder                            } from '../nextflow-modules/modules/serotypefinder/main.nf'
 include { virulencefinder                           } from '../nextflow-modules/modules/virulencefinder/main.nf'
 include { CALL_BACTERIAL_BASE                       } from '../workflows/bacterial_base.nf'
 
@@ -50,7 +49,6 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
     trainingFile = file(params.trainingFile, checkIfExists: true)
     resfinderDb = file(params.resfinderDb, checkIfExists: true)
     pointfinderDb = file(params.pointfinderDb, checkIfExists: true)
-    serotypefinderDb = file(params.serotypefinderDb, checkIfExists: true)
     virulencefinderDb = file(params.virulencefinderDb, checkIfExists: true)
 
     main:
@@ -110,7 +108,6 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         chewbbaca_create_batch_list(maskedAssemblyMap.filePath.collect())
         chewbbaca_allelecall(chewbbaca_create_batch_list.out.list, chewbbacaDb, trainingFile)
         chewbbaca_split_results(maskedAssemblyMap.sampleID.collect(), chewbbaca_allelecall.out.calls)
-        serotypefinder(ch_reads, params.useSerotypeDbs, serotypefinderDb)
 
         // SCREENING
         // antimicrobial detection (amrfinderplus)
@@ -129,8 +126,8 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
             .join(amrfinderplus.out.output)
             .join(resfinder.out.json)
             .join(resfinder.out.meta)
-            .join(serotypefinder.out.json)
-            .join(serotypefinder.out.meta)
+            .join(ch_empty)
+            .join(ch_empty)
             .join(virulencefinder.out.json)
             .join(virulencefinder.out.meta)
             .join(ch_empty)
@@ -178,7 +175,6 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         ch_versions = ch_versions.mix(freebayes.out.versions)
         ch_versions = ch_versions.mix(mlst.out.versions)
         ch_versions = ch_versions.mix(resfinder.out.versions)
-        ch_versions = ch_versions.mix(serotypefinder.out.versions)
         ch_versions = ch_versions.mix(samtools_index_assembly.out.versions)
         ch_versions = ch_versions.mix(virulencefinder.out.versions)
 

diff --git a/workflows/streptococcus_pyogenes.nf b/workflows/streptococcus_pyogenes.nf
@@ -50,8 +50,6 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
     pointfinderDb = file(params.pointfinderDb, checkIfExists: true)
     pubMlstDb = params.pubMlstDb ? file(params.pubMlstDb, checkIfExists: true) : Channel.of([])
     resfinderDb = file(params.resfinderDb, checkIfExists: true)
-    serotypefinderDb = file(params.serotypefinderDb, checkIfExists: true)
-    shigapassDb = params.shigapassDb ? file(params.shigapassDb, checkIfExists: true) : Channel.of([])
     trainingFile = params.trainingFile ? file(params.trainingFile, checkIfExists: true) : Channel.of([])
     virulencefinderDb = file(params.virulencefinderDb, checkIfExists: true)
     // schemas and values
@@ -117,7 +115,6 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
         chewbbaca_allelecall(chewbbaca_create_batch_list.out.list, chewbbacaDb, trainingFile)
         chewbbaca_split_results(maskedAssemblyMap.sampleID.collect(), chewbbaca_allelecall.out.calls)
         emmtyper(ch_assembly)
-        serotypefinder(ch_reads, params.useSerotypeDbs, serotypefinderDb)
 
         // SCREENING
         // antimicrobial detection (amrfinderplus)
@@ -129,27 +126,19 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
-        ch_quast = ch_quast.mix(ch_empty)
-        ch_qc = ch_qc.mix(ch_empty)
-        ch_serotypefinder = serotypefinder.out.json.mix(ch_empty)
-        ch_serotypefinder_meta = serotypefinder.out.meta.mix(ch_empty)
-        ch_shigapass = shigapass.out.csv.mix(ch_empty)
-        ch_ref_bam = ch_ref_bam.mix(ch_empty)
-        ch_ref_bai = ch_ref_bai.mix(ch_empty)
-
         ch_quast
             .join(ch_qc)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
             .join(resfinder.out.json)
             .join(resfinder.out.meta)
-            .join(ch_serotypefinder)
-            .join(ch_serotypefinder_meta)
+            .join(ch_empty)
+            .join(ch_empty)
             .join(virulencefinder.out.json)
             .join(virulencefinder.out.meta)
-            .join(ch_shigapass)
-            .join(ch_emmtyper)
+            .join(ch_empty)
+            .join(emmtyper.out.tsv)
             .join(ch_ref_bam)
             .join(ch_ref_bai)
             .join(ch_metadata)
@@ -187,7 +176,6 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
         ch_versions = ch_versions.mix(freebayes.out.versions)
         ch_versions = ch_versions.mix(mlst.out.versions)
         ch_versions = ch_versions.mix(resfinder.out.versions)
-        ch_versions = ch_versions.mix(serotypefinder.out.versions)
         ch_versions = ch_versions.mix(samtools_index_assembly.out.versions)
         ch_versions = ch_versions.mix(virulencefinder.out.versions)