diff --git a/CHANGELOG.md b/CHANGELOG.md
index b7ab47c2..e12d1d93 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Added module `fastq` to check qc of strep samples
 - Added module `hostile` to remove human reads
 - Added module `sccmec` for typing of SCCmec cassettes in assemblies of Staphylococcus species
+- Added when operators to all modules that aren't in `bacterial_base.nf`
 
 ### Fixed
 
@@ -41,6 +42,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Removed serotypefinder from saureus workflow
 - Fixed jasen running only on the first row/sample in csv
 - Fixed channel problem by changing `Channel.of([])` to `Channel.value([])`
+- Fixed `nextflow.hopper.config` re singularity image path
+- Fixed sccmec version file
+- Fixed handling of ONT samples re fastqc & postalignqc
 
 ### Changed
 
@@ -59,6 +63,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Changed ska & sourmash filepath to symlink dir in `nextflow.hopper.config` & `nextflow.dev.config`
 - Updated Kraken db filepath in `nextflow.hopper.config` & `nextflow.dev.config`
 - Changed `staphylococcus_aureus_all` to `saureus_all` in `Makefile`
+- Moved all when commands to configs
+- Update fastqc & sccmec mem settings
 
 ## [0.9.0]
 
diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
index 675eb046..157bb456 100644
--- a/configs/nextflow.base.config
+++ b/configs/nextflow.base.config
@@ -147,6 +147,7 @@ process {
 	withName: add_igv_track {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
@@ -154,10 +155,12 @@ process {
 		memory = '10.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
 		ext.args = "--plus"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: annotate_delly {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: assembly_trim_clean {
 		container = "${params.containerDir}/perl-json.sif"
@@ -174,13 +177,14 @@ process {
 	withName: bwa_index {
 		container = "${params.containerDir}/bwakit.sif"
 		ext.args = "-M"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_dedup {
 		container = "${params.containerDir}/bwakit.sif"
 		cpus = 16
 		memory = '20.GB'
 		ext.args = "-M"
-		ext.when = true
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_ref {
 		container = "${params.containerDir}/bwakit.sif"
@@ -188,15 +192,20 @@ process {
 		memory = '20.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-M"
-		ext.when = { params.referenceGenome }
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_allelecall {
 		cpus = 16
 		memory = '12.GB'
 		container = "${params.containerDir}/chewbbaca.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
+	}
+	withName: chewbbaca_create_batch_list {
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_split_results {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: create_analysis_result {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -216,6 +225,7 @@ process {
 	withName: emmtyper {
 		container = "${params.containerDir}/emmtyper.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species in ["streptococcus", "streptococcus pyogenes"] }
 	}
 	withName: export_to_cdm {
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
@@ -231,6 +241,7 @@ process {
 	}
 	withName: fastqc {
 		cpus = 4
+		memory = '2.GB'
 		container = "${params.containerDir}/fastqc.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/fastqc", mode: 'copy', overwrite: true ]
 		ext.args = "--threads 4"
@@ -239,6 +250,7 @@ process {
 		container = "${params.containerDir}/freebayes.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-C 2 -F 0.2 --pooled-continuous"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: hostile {
 		container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
@@ -253,6 +265,7 @@ process {
 	}
 	withName: mask_polymorph_assembly {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: medaka {
 		container = "${params.containerDir}/medaka.sif"
@@ -260,17 +273,19 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: mykrobe {
 		memory = '4.GB'
 		container = "${params.containerDir}/mykrobe.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
 		ext.args = "--species tb --format csv"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: nanoplot {
 		container = "${params.containerDir}/nanoplot.sif"
@@ -281,6 +296,7 @@ process {
 		memory = '2.GB'
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "streptococcus" }
 	}
 	withName: quast {
 		container = "${params.containerDir}/quast.sif"
@@ -289,17 +305,20 @@ process {
 	withName: resfinder {
 		container = "${params.containerDir}/resfinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_assembly {
 		cpus = 16
 		memory = '2.GB'
 		container = "${params.containerDir}/samtools.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_ref {
 		cpus = 16
 		memory = '2.GB'
 		container = "${params.containerDir}/samtools.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: save_analysis_metadata {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -308,6 +327,7 @@ process {
 	withName: sccmec {
 		container = "${params.containerDir}/sccmec.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
 	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
@@ -318,11 +338,13 @@ process {
 		cpus = 2
 		container = "${params.containerDir}/serotypefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
+		ext.when = { (params.species in ["escherichia coli", "klebsiella pneumoniae"]) }
 	}
 	withName: shigapass {
 		cpus = 2
 		container = "${params.containerDir}/shigapass.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "escherichia coli" }
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
@@ -344,6 +366,7 @@ process {
 		memory = '32.GB'
 		container = "${params.containerDir}/snippy.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: sourmash {
 		container = "${params.containerDir}/sourmash.sif"
@@ -371,11 +394,13 @@ process {
 		container = "${params.containerDir}/tb-profiler.sif"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: virulencefinder {
 		cpus = 2
 		container = "${params.containerDir}/virulencefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 }
 
diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
index 15f770b6..fa2616a8 100644
--- a/configs/nextflow.ci.config
+++ b/configs/nextflow.ci.config
@@ -135,6 +135,7 @@ process {
 	withName: add_igv_track {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
@@ -142,10 +143,12 @@ process {
 		memory = '10.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ncbi-amrfinderplus", mode: 'copy', overwrite: true ]
 		ext.args = "--plus"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: annotate_delly {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: assembly_trim_clean {
 		container = "${params.containerDir}/perl-json.sif"
@@ -162,13 +165,14 @@ process {
 	withName: bwa_index {
 		container = "${params.containerDir}/bwakit.sif"
 		ext.args = "-M"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_dedup {
 		container = "${params.containerDir}/bwakit.sif"
 		cpus = 4
 		memory = '12.GB'
 		ext.args = "-M"
-		ext.when = true
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_ref {
 		container = "${params.containerDir}/bwakit.sif"
@@ -176,15 +180,20 @@ process {
 		memory = '12.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-M"
-		ext.when = { params.referenceGenome }
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_allelecall {
 		cpus = 4
 		memory = '12.GB'
 		container = "${params.containerDir}/chewbbaca.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
+	}
+	withName: chewbbaca_create_batch_list {
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_split_results {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: create_analysis_result {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -204,20 +213,32 @@ process {
 	withName: emmtyper {
 		container = "${params.containerDir}/emmtyper.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species in ["streptococcus", "streptococcus pyogenes"] }
 	}
 	withName: export_to_cdm {
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
 	}
 	withName: fastqc {
 		cpus = 4
+		memory = '2.GB'
 		container = "${params.containerDir}/fastqc.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/fastqc", mode: 'copy', overwrite: true ]
 		ext.args = "--threads 4"
 	}
+	withName: flye {
+		container = "${params.containerDir}/flye.sif"
+		cpus = 4
+		memory = '2.GB'
+		time=2.h
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/flye", mode: 'copy', overwrite: true ]
+		ext.args = "--threads 40 --genome-size 2.8m --asm-coverage 50"
+		ext.seqmethod = "--nano-hq"
+	}
 	withName: freebayes {
 		container = "${params.containerDir}/freebayes.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-C 2 -F 0.2 --pooled-continuous"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: hostile {
 		container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
@@ -232,6 +253,7 @@ process {
 	}
 	withName: mask_polymorph_assembly {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: medaka {
 		container = "${params.containerDir}/medaka.sif"
@@ -239,17 +261,19 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: mykrobe {
 		memory = '4.GB'
 		container = "${params.containerDir}/mykrobe.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
 		ext.args = "--species tb --format csv"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: nanoplot {
 		container = "${params.containerDir}/nanoplot.sif"
@@ -260,6 +284,7 @@ process {
 		memory = '2.GB'
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "streptococcus" }
 	}
 	withName: quast {
 		container = "${params.containerDir}/quast.sif"
@@ -268,17 +293,20 @@ process {
 	withName: resfinder {
 		container = "${params.containerDir}/resfinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_assembly {
 		cpus = 4
 		memory = '2.GB'
 		container = "${params.containerDir}/samtools.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_ref {
 		cpus = 4
 		memory = '2.GB'
 		container = "${params.containerDir}/samtools.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: save_analysis_metadata {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -287,6 +315,7 @@ process {
 	withName: sccmec {
 		container = "${params.containerDir}/sccmec.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
 	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
@@ -297,11 +326,13 @@ process {
 		cpus = 2
 		container = "${params.containerDir}/serotypefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
+		ext.when = { (params.species in ["escherichia coli", "klebsiella pneumoniae"]) }
 	}
 	withName: shigapass {
 		cpus = 2
 		container = "${params.containerDir}/shigapass.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "escherichia coli" }
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
@@ -323,6 +354,7 @@ process {
 		memory = '12.GB'
 		container = "${params.containerDir}/snippy.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: sourmash {
 		container = "${params.containerDir}/sourmash.sif"
@@ -350,11 +382,13 @@ process {
 		container = "${params.containerDir}/tb-profiler.sif"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: virulencefinder {
 		cpus = 2
 		container = "${params.containerDir}/virulencefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 }
 
diff --git a/configs/nextflow.dev.config b/configs/nextflow.cmd.config
similarity index 86%
rename from configs/nextflow.dev.config
rename to configs/nextflow.cmd.config
index da9a4dda..53367e26 100644
--- a/configs/nextflow.dev.config
+++ b/configs/nextflow.cmd.config
@@ -1,4 +1,4 @@
-// Hopper specific configuration for micro wgs pipeline //
+// Configuration for the Centre of Molecular Diagnostics (CMD) in Lund, Sweden //
 
 params {
 	root = "/fs1/pipelines/jasen_dev"
@@ -18,6 +18,7 @@ params {
 	scratch = true
 	containerDir = "/fs1/resources/containers"
 	outdir = "/fs1/results_dev/jasen"
+	bonsaiPrpSif = "${params.containerDir}/bonsai-prp.sif"
 	args = ""
 	prefix = ""
 	bamDir = "bam"
@@ -26,7 +27,7 @@ params {
 	// PIPELINE OPTIONS //
 	devMode = true
 	cronCopy = false
-	useHostile = false
+	useHostile = true
 	useKraken = true
 	useSkesa = true // To use spades set useSkesa = false
 	queue='grace-high'
@@ -93,9 +94,9 @@ profiles {
 	mycobacterium_tuberculosis {
 		params.species = 'mycobacterium tuberculosis'
 		params.speciesDir = 'mtuberculosis'
-		params.symlinkDir = "/access/jasen/mtuberculosis/"
 		params.resistantLociName = 'resistance_loci'
 		params.gradingLociName = 'grading_loci'
+		params.symlinkDir = "/access/jasen/mtuberculosis/"
 		params.referenceGenome = "${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"
@@ -137,6 +138,22 @@ profiles {
 		params.useSerotypeDbs = []
 		params.targetSampleSize = null
 	}
+
+	dev {
+		params.root = "/fs1/pipelines/jasen_dev"
+		params.outdir = "/fs1/results_dev/jasen"
+		params.devMode = true
+		params.cronCopy = false
+		params.bonsaiPrpSif = "${params.containerDir}/bonsai-prp.sif"
+	}
+
+	production {
+		params.root = "/fs1/pipelines/jasen"
+		params.outdir = "/fs1/results/jasen"
+		params.devMode = false
+		params.cronCopy = true
+		params.bonsaiPrpSif = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
+	}
 }
 
 process {
@@ -147,8 +164,9 @@ process {
 	cpus=2
 
 	withName: add_igv_track {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: amrfinderplus {
 		container = "https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0"
@@ -156,10 +174,12 @@ process {
 		memory = '10.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
 		ext.args = "--plus"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: annotate_delly {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: assembly_trim_clean {
 		container = "https://depot.galaxyproject.org/singularity/perl-json:4.10--pl5321hdfd78af_0"
@@ -176,13 +196,14 @@ process {
 	withName: bwa_index {
 		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
 		ext.args = "-M"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_dedup {
 		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
 		cpus = 16
 		memory = '20.GB'
 		ext.args = "-M"
-		ext.when = true
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_ref {
 		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
@@ -190,26 +211,31 @@ process {
 		memory = '20.GB'
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-M"
-		ext.when = { params.referenceGenome }
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_allelecall {
 		cpus = 16
 		memory = '12.GB'
 		container = "https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
+	}
+	withName: chewbbaca_create_batch_list {
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_split_results {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: create_analysis_result {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
 	}
 	withName: create_cdm_input {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
 		ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
 		ext.args_sourmash = {"/access/jasen/${params.speciesDir}/sourmash"}
@@ -218,6 +244,7 @@ process {
 	withName: emmtyper {
 		container = "https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species in ["streptococcus", "streptococcus pyogenes"] }
 	}
 	withName: export_to_cdm {
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
@@ -241,6 +268,7 @@ process {
 		container = "https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-C 2 -F 0.2 --pooled-continuous"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: hostile {
 		container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
@@ -255,6 +283,7 @@ process {
 	}
 	withName: mask_polymorph_assembly {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: medaka {
 		container = "https://depot.galaxyproject.org/singularity/medaka:1.11.3--py39h05d5c5e_0"
@@ -262,17 +291,19 @@ process {
 		memory = '32.GB'
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
+		ext.args = "-t 40 -m r941_min_sup_g507"
 	}
 	withName: mlst {
 		container = "https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: mykrobe {
 		memory = '4.GB'
 		container = "https://depot.galaxyproject.org/singularity/mykrobe:0.12.2--py39h70e0db4_0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
 		ext.args = "--species tb --format csv"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: nanoplot {
 		container = "https://depot.galaxyproject.org/singularity/nanoplot:1.43.0--pyhdfd78af_1"
@@ -281,8 +312,9 @@ process {
 	}
 	withName: post_align_qc {
 		memory = '2.GB'
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "streptococcus" }
 	}
 	withName: quast {
 		container = "https://depot.galaxyproject.org/singularity/quast:5.2.0--py310pl5321hc8f18ef_2"
@@ -291,25 +323,31 @@ process {
 	withName: resfinder {
 		container = "https://depot.galaxyproject.org/singularity/resfinder:4.4.2--pyhdfd78af_1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_assembly {
 		cpus = 16
 		memory = '2.GB'
 		container = "https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_ref {
 		cpus = 16
 		memory = '2.GB'
 		container = "https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: save_analysis_metadata {
-		container = "${params.containerDir}/bonsai-prp.sif"
+		container = "${params.bonsaiPrpSif}"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
 	}
 	withName: sccmec {
+		cpus = 2
+		memory = '2.GB'
 		container = "https://depot.galaxyproject.org/singularity/sccmec:1.2.0--hdfd78af_0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
 	}
 	withName: seqtk_sample {
 		container = "https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2"
@@ -320,11 +358,13 @@ process {
 		cpus = 2
 		container = "https://depot.galaxyproject.org/singularity/serotypefinder:2.0.2--py312hdfd78af_1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
+		ext.when = { (params.species in ["escherichia coli", "klebsiella pneumoniae"]) }
 	}
 	withName: shigapass {
 		cpus = 2
 		container = "https://depot.galaxyproject.org/singularity/shigapass:1.5.0--hdfd78af_0"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "escherichia coli" }
 	}
 	withName: ska_build {
 		container = "https://depot.galaxyproject.org/singularity/ska2:0.3.10--h4349ce8_0"
@@ -346,6 +386,7 @@ process {
 		memory = '32.GB'
 		container = "https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: sourmash {
 		container = "https://depot.galaxyproject.org/singularity/sourmash:4.8.2--hdfd78af_0"
@@ -373,11 +414,13 @@ process {
 		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: virulencefinder {
 		cpus = 2
 		container = "https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4--hdfd78af_1"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	
 }
diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
deleted file mode 100644
index 312f62c8..00000000
--- a/configs/nextflow.hopper.config
+++ /dev/null
@@ -1,388 +0,0 @@
-// Hopper specific configuration for micro wgs pipeline //
-
-params {
-	root = "/fs1/pipelines/jasen"
-	// DATABASES //
-	amrfinderDb = "${root}/assets/amrfinder_db/latest"
-	resfinderDb = "${root}/assets/resfinder_db"
-	pointfinderDb = "${root}/assets/pointfinder_db"
-	serotypefinderDb = "${root}/assets/serotypefinder_db"
-	virulencefinderDb = "${root}/assets/virulencefinder_db"
-	mlstBlastDb = "${root}/assets/mlst_db/blast"
-	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
-	krakenDb = "/fs1/resources/ref/micro/k2_standard_20240904"
-	// INPUT & OUTPUT //
-	publishDir = ""
-	publishDirMode = 'copy'
-	publishDirOverwrite = true
-	scratch = true
-	containerDir = "/fs1/resources/containers"
-	outdir = "/fs1/results/jasen"
-	args = ""
-	prefix = ""
-	bamDir = "bam"
-	cdmDir = "cdm_input"
-	vcfDir = "vcf"
-	// PIPELINE OPTIONS //
-	cronCopy = true
-	useHostile = false
-	useKraken = true
-	useSkesa = true // To use spades set useSkesa = false
-	queue='grace-high'
-}
-
-singularity{
-	enabled = true
-	runOptions = '--bind /fs1/ --bind /fs2/ --bind /local/ --bind /mnt/beegfs/'
-	cacheDir = "${params.containerDir}/"
-}
-
-profiles {
-	staphylococcus_aureus {
-		params.species = "staphylococcus aureus"
-		params.speciesDir = 'saureus'
-		params.mlstScheme = 'saureus'
-		params.symlinkDir = "/access/jasen/saureus/"
-		params.referenceGenome = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta"
-		params.referenceGenomeIdx = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.fasta.fai"
-		params.referenceGenomeGff = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff"
-		params.chewbbacaDb = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed"
-		params.coreLociBed = "${params.root}/assets/cgmlst/staphylococcus_aureus/bed/GCF_000012045.1.bed"
-		params.trainingFile = "${params.root}/assets/cgmlst/staphylococcus_aureus/alleles_rereffed/Staphylococcus_aureus.trn"
-		params.useVirulenceDbs = ['s.aureus_hostimm', 's.aureus_exoenzyme', 's.aureus_toxin']
-		params.useSerotypeDbs = []
-		params.targetSampleSize = null
-	}
-
-	escherichia_coli {
-		params.species = 'escherichia coli'
-		params.speciesDir = 'ecoli'
-		params.mlstScheme = 'ecoli_achtman_4'
-		params.symlinkDir = "/access/jasen/ecoli/"
-		params.referenceGenome = "${params.root}/assets/genomes/escherichia_coli/GCF_000005845.2.fasta"
-		params.referenceGenomeIdx = "${params.root}/assets/genomes/escherichia_coli/GCF_000005845.2.fasta.fai"
-		params.referenceGenomeGff = "${params.root}/assets/genomes/escherichia_coli/GCF_000005845.2.gff"
-		// params.chewbbacaDb = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed"
-		// params.coreLociBed = "${params.root}/assets/cgmlst/escherichia_coli/bed/GCF_000005845.2.bed"
-		// params.trainingFile = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn"
-		params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST"
-		params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed"
-		params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases"
-		params.trainingFile = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST/Escherichia_coli.trn"
-		params.useVirulenceDbs = ['virulence_ecoli', 'stx']
-		params.useSerotypeDbs = ['O_type', 'H_type']
-		params.targetSampleSize = null
-	}
-
-	klebsiella_pneumoniae {
-		params.species = 'klebsiella pneumoniae'
-		params.speciesDir = 'kpneumoniae'
-		params.mlstScheme = 'klebsiella'
-		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 = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff"
-		params.chewbbacaDb = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed"
-		params.coreLociBed = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/bed/GCF_000240185.1.bed"
-		params.trainingFile = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn"
-		params.useVirulenceDbs = []
-		params.useSerotypeDbs = ['O_type', 'H_type']
-		params.targetSampleSize = null
-	}
-
-	mycobacterium_tuberculosis {
-		params.species = 'mycobacterium tuberculosis'
-		params.speciesDir = 'mtuberculosis'
-		params.resistantLociName = 'resistance_loci'
-		params.gradingLociName = 'grading_loci'
-		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 = "${params.root}/assets/genomes/mycobacterium_tuberculosis/GCF_000195955.2.gff"
-		params.coreLociBed = "${params.root}/assets/cgmlst/mycobacterium_tuberculosis/bed/GCF_000195955.2.bed"
-		params.tbGradingRulesBed = "${params.root}/assets/tb_info/bed/tb_grading_rules.bed"
-		params.tbdbBed = "${params.root}/assets/tbdb/converged_who_fohm_tbdb.bed.gz"
-		params.tbdbBedIdx = "${params.tbdbBed}.tbi"
-		params.targetSampleSize = null
-	}
-
-	streptococcus_pyogenes {
-		params.species = 'streptococcus pyogenes'
-		params.speciesDir = 'spyogenes'
-		params.mlstScheme = 'spyogenes'
-		params.symlinkDir = "/access/jasen/spyogenes/"
-		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta"
-		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.fasta.fai"
-		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
-		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
-		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_900475035.1.bed"
-		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
-		params.useVirulenceDbs = []
-		params.useSerotypeDbs = []
-		params.targetSampleSize = null
-	}
-
-	streptococcus {
-		params.species = 'streptococcus'
-		params.speciesDir = 'streptococcus'
-		params.mlstScheme = null
-		params.referenceGenome = null
-		params.referenceGenomeIdx = null
-		params.referenceGenomeGff = null
-		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
-		params.shigapassDb = null
-		params.coreLociBed = null
-		params.trainingFile = null
-		params.useVirulenceDbs = []
-		params.useSerotypeDbs = []
-		params.targetSampleSize = null
-	}
-}
-
-process {
-	executor='slurm'
-	queue=params.queue
-	time=1.h
-	memory='1.GB'
-	cpus=2
-
-	withName: add_igv_track {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
-	}
-	withName: amrfinderplus {
-		container = "https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.11.11--h6e70893_0"
-		cpus = 4
-		memory = '10.GB'
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
-		ext.args = "--plus"
-	}
-	withName: annotate_delly {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
-	}
-	withName: assembly_trim_clean {
-		container = "https://depot.galaxyproject.org/singularity/perl-json:4.10--pl5321hdfd78af_0"
-		cpus = 4
-		memory = '10.GB'
-		ext.args = "--min_quality 23 --bases_to_trim 400 --min_length 100 -p 1 --nosingletons"
-	}
-	withName: bracken {
-		container = "https://depot.galaxyproject.org/singularity/bracken:2.8--py39hc16433a_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/kraken", mode: 'copy', overwrite: true ]
-		ext.args = "-r 150"
-		ext.when = { params.useKraken }
-	}
-	withName: bwa_index {
-		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
-		ext.args = "-M"
-	}
-	withName: bwa_mem_dedup {
-		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
-		cpus = 16
-		memory = '20.GB'
-		ext.args = "-M"
-		ext.when = true
-	}
-	withName: bwa_mem_ref {
-		container = "https://depot.galaxyproject.org/singularity/bwakit:0.7.17.dev1--hdfd78af_1"
-		cpus = 16
-		memory = '20.GB'
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
-		ext.args = "-M"
-		ext.when = { params.referenceGenome }
-	}
-	withName: chewbbaca_allelecall {
-		cpus = 16
-		memory = '12.GB'
-		container = "https://depot.galaxyproject.org/singularity/chewbbaca:3.3.2--pyhdfd78af_0"
-	}
-	withName: chewbbaca_split_results {
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
-	}
-	withName: create_analysis_result {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
-	}
-	withName: create_cdm_input {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
-	}
-	withName: create_yaml {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/analysis_yaml", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/jasen/${params.speciesDir}", mode: 'copy', overwrite: true ] ] : [])
-		ext.args_prp = {"${params.outdir}/${params.speciesDir}/analysis_result"}
-		ext.args_sourmash = {"/access/jasen/${params.speciesDir}/sourmash"}
-		ext.args_ska = {"/access/jasen/${params.speciesDir}/ska"}
-	}
-	withName: emmtyper {
-		container = "https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
-	}
-	withName: export_to_cdm {
-		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
-	}
-	withName: flye {
-		container = "https://depot.galaxyproject.org/singularity/flye:2.9.3--py39hd65a603_0"
-		cpus = 20
-		memory = '32.GB'
-		time=2.h
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/flye", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 --genome-size 2.8m --asm-coverage 50"
-	}
-	withName: fastqc {
-		cpus = 4
-		container = "https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/fastqc", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 4"
-	}
-	withName: freebayes {
-		container = "https://depot.galaxyproject.org/singularity/freebayes:1.3.6--hbfe0e7f_2"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
-		ext.args = "-C 2 -F 0.2 --pooled-continuous"
-	}
-	withName: hostile {
-		container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
-		ext.when = { params.useHostile }
-	}
-	withName: kraken {
-		memory = '100.GB'
-		cpus = 16
-		container = "https://depot.galaxyproject.org/singularity/kraken2:2.1.2--pl5321h9f5acd7_3"
-		ext.args = "--gzip-compressed"
-		ext.when = { params.useKraken }
-	}
-	withName: mask_polymorph_assembly {
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
-	}
-	withName: medaka {
-		container = "https://depot.galaxyproject.org/singularity/medaka:1.11.3--py39h05d5c5e_0"
-		cpus = 20
-		memory = '32.GB'
-		time=2.h
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 40 -m r941_min_sup_g507"
-	}
-	withName: mlst {
-		container = "https://depot.galaxyproject.org/singularity/mlst:2.23.0--hdfd78af_1"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
-	}
-	withName: mykrobe {
-		memory = '4.GB'
-		container = "https://depot.galaxyproject.org/singularity/mykrobe:0.12.2--py39h70e0db4_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
-		ext.args = "--species tb --format csv"
-	}
-	withName: nanoplot {
-		container = "https://depot.galaxyproject.org/singularity/nanoplot:1.43.0--pyhdfd78af_1"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/nanoplot", mode: 'copy', overwrite: true ]
-		ext.args = "--threads 8"
-	}
-	withName: post_align_qc {
-		memory = '2.GB'
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
-	}
-	withName: quast {
-		container = "https://depot.galaxyproject.org/singularity/quast:5.2.0--py310pl5321hc8f18ef_2"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/quast", mode: 'copy', overwrite: true ]
-	}
-	withName: resfinder {
-		container = "https://depot.galaxyproject.org/singularity/resfinder:4.4.2--pyhdfd78af_1"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
-	}
-	withName: samtools_index_assembly {
-		cpus = 16
-		memory = '2.GB'
-		container = "https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0"
-	}
-	withName: samtools_index_ref {
-		cpus = 16
-		memory = '2.GB'
-		container = "https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
-	}
-	withName: save_analysis_metadata {
-		container = "docker://clinicalgenomicslund/bonsai-prp:0.11.4"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_metadata", mode: 'copy', overwrite: true ]
-	}
-	withName: sccmec {
-		container = "https://depot.galaxyproject.org/singularity/sccmec:1.2.0--hdfd78af_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
-	}
-	withName: seqtk_sample {
-		container = "https://depot.galaxyproject.org/singularity/seqtk:1.4--he4a0461_2"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/seqtk_sample", mode: 'copy', overwrite: true ]
-		ext.when = { params.targetSampleSize ? true : false }
-	}
-	withName: serotypefinder {
-		cpus = 2
-		container = "https://depot.galaxyproject.org/singularity/serotypefinder:2.0.2--py312hdfd78af_1"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
-	}
-	withName: shigapass {
-		cpus = 2
-		container = "https://depot.galaxyproject.org/singularity/shigapass:1.5.0--hdfd78af_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
-	}
-	withName: ska_build {
-		container = "https://depot.galaxyproject.org/singularity/ska2:0.3.10--h4349ce8_0"
-		cpus = 2
-		memory = '10.GB'
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/ska", mode: 'copy', overwrite: true ]
-		ext.args = "-k 31 --threads 1"
-	}
-	withName: skesa {
-		container = "https://depot.galaxyproject.org/singularity/skesa:2.4.0--he1c1bb9_0"
-		cpus = 16
-		memory = '32.GB'
-		time=2.h
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/skesa", mode: 'copy', overwrite: true ]
-		ext.args = "--cores 16 --memory 32"
-		ext.when = { params.useSkesa }
-	}
-	withName: snippy {
-		memory = '32.GB'
-		container = "https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
-	}
-	withName: sourmash {
-		container = "https://depot.galaxyproject.org/singularity/sourmash:4.8.2--hdfd78af_0"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sourmash", mode: 'copy', overwrite: true ]
-		ext.args = "-p k=31,k=51,scaled=1000"
-	}
-	withName: spades_illumina {
-		container = "https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1"
-		cpus = 16
-		memory = '15.GB'
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_illumina", mode: 'copy', overwrite: true ]
-		ext.args = "--isolate"
-		ext.when = { !params.useSkesa }
-	}
-	withName: spades_iontorrent {
-		container = "https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1"
-		cpus = 16
-		memory = '15.GB'
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/spades_iontorrent", mode: 'copy', overwrite: true ]
-		ext.args = "--iontorrent --careful --sc"
-	}
-	withName: tbprofiler_mergedb {
-		cpus = 16
-		memory = '12.GB'
-		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.3.0--pyhdfd78af_0"
-		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
-		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
-	}
-	withName: virulencefinder {
-		cpus = 2
-		container = "https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4--hdfd78af_1"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
-	}
-}
-
-manifest {
-	homePage = 'https://github.com/genomic-medicine-sweden/jasen'
-	description = 'Pipeline epitypes numerous bacterial species as well as identifies AMR and virulence genes'
-	mainScript = 'main.nf'
-	version = '0.9.0'
-}
diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
index 253b1783..34f27748 100644
--- a/configs/nextflow.ngp.config
+++ b/configs/nextflow.ngp.config
@@ -160,6 +160,7 @@ process {
 	withName: add_igv_track {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/analysis_result", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: amrfinderplus {
 		container = "${params.containerDir}/ncbi-amrfinderplus.sif"
@@ -167,10 +168,12 @@ process {
 		memory = params.mem_medium
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/amrfinderplus", mode: 'copy', overwrite: true ]
 		ext.args = "--plus"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: annotate_delly {
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: assembly_trim_clean {
 		container = "${params.containerDir}/perl-json.sif"
@@ -187,13 +190,14 @@ process {
 	withName: bwa_index {
 		container = "${params.containerDir}/bwakit.sif"
 		ext.args = "-M"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_dedup {
 		container = "${params.containerDir}/bwakit.sif"
 		cpus = params.cpus_large
 		memory = params.mem_large
 		ext.args = "-M"
-		ext.when = true
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: bwa_mem_ref {
 		container = "${params.containerDir}/bwakit.sif"
@@ -201,15 +205,20 @@ process {
 		memory = params.mem_large
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-M"
-		ext.when = { params.referenceGenome }
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_allelecall {
 		cpus = params.cpus_large
 		memory = params.mem_large
 		container = "${params.containerDir}/chewbbaca.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
+	}
+	withName: chewbbaca_create_batch_list {
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: chewbbaca_split_results {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/chewbbaca", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: create_analysis_result {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -229,21 +238,33 @@ process {
 	withName: emmtyper {
 		container = "${params.containerDir}/emmtyper.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/emmtyper", mode: 'copy', overwrite: true ]
+		ext.when = { params.species in ["streptococcus", "streptococcus pyogenes"] }
 	}
 	withName: export_to_cdm {
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/qc", mode: 'copy', overwrite: true ] ] + (params.cronCopy ? [ [ path: "/fs1/results/cron/qc", mode: 'copy', overwrite: true ] ] : [])
 	}
 	withName: fastqc {
-		cpus = 4
+		cpus = params.cpus_small
+		memory = params.mem_small
 		container = "${params.containerDir}/fastqc.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/fastqc", mode: 'copy', overwrite: true ]
 		ext.args = "--threads 4"
 	}
+	withName: flye {
+		container = "${params.containerDir}/flye.sif"
+		cpus = params.cpus_large
+		memory = params.mem_large
+		time=2.h
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/flye", mode: 'copy', overwrite: true ]
+		ext.args = "--threads 40 --genome-size 2.8m --asm-coverage 50"
+		ext.seqmethod = "--nano-hq"
+	}
 	withName: freebayes {
 		cpus = params.cpus_small
 		container = "${params.containerDir}/freebayes.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true ]
 		ext.args = "-C 2 -F 0.2 --pooled-continuous"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: hostile {
 		container = "https://depot.galaxyproject.org/singularity/hostile:2.0.0--pyhdfd78af_0"
@@ -259,11 +280,12 @@ process {
 	}
 	withName: mask_polymorph_assembly {
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mask", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: medaka {
 		container = "${params.containerDir}/medaka.sif"
-		cpus = 20
-		memory = '32.GB'
+		cpus = params.cpus_large
+		memory = params.mem_large
 		time=2.h
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/medaka", mode: 'copy', overwrite: true ]
 		ext.args = "--threads 40 -m r941_min_sup_g507"
@@ -271,6 +293,7 @@ process {
 	withName: mlst {
 		container = "${params.containerDir}/mlst.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mlst", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: mykrobe {
 		cpus = params.cpus_medium
@@ -278,6 +301,7 @@ process {
 		container = "${params.containerDir}/mykrobe.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/mykrobe", mode: 'copy', overwrite: true ]
 		ext.args = "--species tb --format csv"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: nanoplot {
 		container = "${params.containerDir}/nanoplot.sif"
@@ -289,6 +313,7 @@ process {
 		memory = params.mem_small
 		container = "${params.containerDir}/bonsai-prp.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/postalignqc", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "streptococcus" }
 	}
 	withName: quast {
 		container = "${params.containerDir}/quast.sif"
@@ -297,17 +322,20 @@ process {
 	withName: resfinder {
 		container = "${params.containerDir}/resfinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/resfinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_assembly {
 		cpus = params.cpus_large
 		memory = params.mem_large
 		container = "${params.containerDir}/samtools.sif"
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 	withName: samtools_index_ref {
 		cpus = params.cpus_large
 		memory = params.mem_large
 		container = "${params.containerDir}/samtools.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true ]
+		ext.when = { params.referenceGenome && params.species != "mycobacterium tuberculosis" }
 	}
 	withName: save_analysis_metadata {
 		container = "${params.containerDir}/bonsai-prp.sif"
@@ -316,6 +344,7 @@ process {
 	withName: sccmec {
 		container = "${params.containerDir}/sccmec.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/sccmec", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "staphylococcus aureus" }
 	}
 	withName: seqtk_sample {
 		container = "${params.containerDir}/seqtk.sif"
@@ -326,11 +355,13 @@ process {
 		cpus = params.cpus_small
 		container = "${params.containerDir}/serotypefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/serotypefinder", mode: 'copy', overwrite: true ]
+		ext.when = { (params.species in ["escherichia coli", "klebsiella pneumoniae"]) }
 	}
 	withName: shigapass {
 		cpus = params.cpus_small
 		container = "${params.containerDir}/shigapass.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/shigapass", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "escherichia coli" }
 	}
 	withName: ska_build {
 		container = "${params.containerDir}/ska2.sif"
@@ -353,6 +384,7 @@ process {
 		memory = params.mem_large
 		container = "${params.containerDir}/snippy.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/snippy", mode: 'copy', overwrite: true ]
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: sourmash {
 		container = "${params.containerDir}/sourmash.sif"
@@ -380,12 +412,14 @@ process {
 		container = "${params.containerDir}/tb-profiler.sif"
 		publishDir = [ [ path: "${params.outdir}/${params.speciesDir}/tbprofiler_mergedb", mode: 'copy', overwrite: true, pattern: '*.json' ], [ path: "${params.outdir}/${params.speciesDir}/${params.vcfDir}", mode: 'copy', overwrite: true, pattern: '*.{vcf.gz}' ], [ path: "${params.outdir}/${params.speciesDir}/${params.bamDir}", mode: 'copy', overwrite: true, pattern: '*.bam*' ] ]
 		ext.args = "--external_db ${params.root}/assets/tbdb/converged_who_fohm_tbdb --calling_params '-q 15'"
+		ext.when = { params.species == "mycobacterium tuberculosis" }
 	}
 	withName: virulencefinder {
 		cpus = params.cpus_small
 		memory = params.mem_small
 		container = "${params.containerDir}/virulencefinder.sif"
 		publishDir = [ path: "${params.outdir}/${params.speciesDir}/virulencefinder", mode: 'copy', overwrite: true ]
+		ext.when = { params.species != "mycobacterium tuberculosis" }
 	}
 }
 
diff --git a/main.nf b/main.nf
index 74ef75a6..e44fce07 100644
--- a/main.nf
+++ b/main.nf
@@ -10,17 +10,17 @@ include { CALL_STREPTOCOCCUS_PYOGENES       } from './workflows/streptococcus_py
 include { CALL_STREPTOCOCCUS                } from './workflows/streptococcus.nf'
 
 workflow {
-    if (workflow.profile == "staphylococcus_aureus") {
+    if (params.species == "staphylococcus aureus") {
         CALL_STAPHYLOCOCCUS_AUREUS()
-    } else if (workflow.profile == "mycobacterium_tuberculosis") {
+    } else if (params.species == "mycobacterium tuberculosis") {
         CALL_MYCOBACTERIUM_TUBERCULOSIS()
-    } else if (workflow.profile == "klebsiella_pneumoniae") {
+    } else if (params.species == "klebesiella pneumoniae") {
         CALL_KLEBSIELLA_PNEUMONIAE()
-    } else if (workflow.profile == "escherichia_coli") {
+    } else if (params.species == "escherichia coli") {
         CALL_ESCHERICHIA_COLI()
-    } else if (workflow.profile == "streptococcus_pyogenes") {
+    } else if (params.species == "streptococcus pyogenes") {
         CALL_STREPTOCOCCUS_PYOGENES()
-    } else if (workflow.profile == "streptococcus") {
+    } else if (params.species == "streptococcus") {
         CALL_STREPTOCOCCUS()
     }
 }
diff --git a/nextflow-modules/modules/amrfinderplus/main.nf b/nextflow-modules/modules/amrfinderplus/main.nf
index a9604d13..4769407d 100644
--- a/nextflow-modules/modules/amrfinderplus/main.nf
+++ b/nextflow-modules/modules/amrfinderplus/main.nf
@@ -13,6 +13,9 @@ process amrfinderplus {
     tuple val(sample_id), path(output), emit: output
     path "*versions.yml"             , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     def args = task.ext.args ?: ''
     def database_arg = database ? "--database ${database}" : ""
diff --git a/nextflow-modules/modules/bwa/main.nf b/nextflow-modules/modules/bwa/main.nf
index af2b3ef4..6a588e31 100644
--- a/nextflow-modules/modules/bwa/main.nf
+++ b/nextflow-modules/modules/bwa/main.nf
@@ -10,7 +10,7 @@ process bwa_index {
     path "*versions.yml"                        , emit: versions
 
   when:
-    workflow.profile != "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     """
@@ -54,7 +54,7 @@ process bwa_mem {
     path "*versions.yml"             , emit: versions
 
   when:
-    task.ext.when && workflow.profile != "mycobacterium_tuberculosis" 
+    task.ext.when
 
   script:
     def args = task.ext.args ?: ''
diff --git a/nextflow-modules/modules/chewbbaca/main.nf b/nextflow-modules/modules/chewbbaca/main.nf
index b4973106..111a060a 100644
--- a/nextflow-modules/modules/chewbbaca/main.nf
+++ b/nextflow-modules/modules/chewbbaca/main.nf
@@ -11,6 +11,9 @@ process chewbbaca_allelecall {
     path('output_dir/results_alleles.tsv'), emit: calls
     path "*versions.yml"                  , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     def args = task.ext.args ?: ''
     training_file = training_file ? "--ptf ${training_file}" : "" 
@@ -54,6 +57,9 @@ process chewbbaca_create_batch_list {
   output:
     path "batch_input.list", emit: list
 
+  when:
+    task.ext.when
+
   script:
     output = "batch_input.list"
     """
@@ -78,6 +84,9 @@ process chewbbaca_split_results {
   output:
     tuple val(sample_id), path(output), emit: output
 
+  when:
+    task.ext.when
+
   script:
     output = "${sample_id}_chewbbaca.out"
     """
diff --git a/nextflow-modules/modules/emmtyper/main.nf b/nextflow-modules/modules/emmtyper/main.nf
index 28128076..f5e7c0d1 100644
--- a/nextflow-modules/modules/emmtyper/main.nf
+++ b/nextflow-modules/modules/emmtyper/main.nf
@@ -10,7 +10,7 @@ process emmtyper {
     path "*versions.yml"              , emit: versions
 
   when:
-    workflow.profile in ["streptococcus", "streptococcus_pyogenes"]
+    task.ext.when
 
   script:
     def args = task.ext.args ?: ''
diff --git a/nextflow-modules/modules/fastqc/main.nf b/nextflow-modules/modules/fastqc/main.nf
index 3ba0e05d..3fa85b89 100644
--- a/nextflow-modules/modules/fastqc/main.nf
+++ b/nextflow-modules/modules/fastqc/main.nf
@@ -3,7 +3,7 @@ process fastqc {
   scratch params.scratch
 
   input:
-    tuple val(sample_id), path(reads)
+    tuple val(sample_id), path(reads), val(platform)
 
   output:
     tuple val(sample_id), path(summary_output), emit: summary
@@ -11,6 +11,9 @@ process fastqc {
     tuple val(sample_id), path(html_output)   , emit: html
     path "*versions.yml"                      , emit: versions
 
+  when:
+    platform == "illumina"
+
   script:
     def args          = task.ext.args ?: ''
     def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${sample_id}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${sample_id}_${index + 1}.${entry.extension}" ] }
diff --git a/nextflow-modules/modules/freebayes/main.nf b/nextflow-modules/modules/freebayes/main.nf
index 8f66a0c3..9c5b1f59 100644
--- a/nextflow-modules/modules/freebayes/main.nf
+++ b/nextflow-modules/modules/freebayes/main.nf
@@ -10,6 +10,9 @@ process freebayes {
     tuple val(sample_id), path(output), emit: vcf
     path "*versions.yml"              , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     def args = task.ext.args ?: ''
     output = "${sample_id}_freebayes.vcf"
diff --git a/nextflow-modules/modules/mask/main.nf b/nextflow-modules/modules/mask/main.nf
index 5c40359d..4ac950a1 100644
--- a/nextflow-modules/modules/mask/main.nf
+++ b/nextflow-modules/modules/mask/main.nf
@@ -8,6 +8,9 @@ process mask_polymorph_assembly {
   output:
     tuple val(sample_id), path(output), emit: fasta
 
+  when:
+    task.ext.when
+
   script:
     output = "${sample_id}_mask.fasta"
     """
diff --git a/nextflow-modules/modules/mlst/main.nf b/nextflow-modules/modules/mlst/main.nf
index d26b07aa..c68649fe 100644
--- a/nextflow-modules/modules/mlst/main.nf
+++ b/nextflow-modules/modules/mlst/main.nf
@@ -8,6 +8,9 @@ process mlst {
     path pbmlst_db
     path blast_db
 
+  when:
+    task.ext.when
+
   output:
     tuple val(sample_id), path('*.tsv')  , optional: true, emit: tsv
     tuple val(sample_id), path('*.json') , optional: true, emit: json
diff --git a/nextflow-modules/modules/mykrobe/main.nf b/nextflow-modules/modules/mykrobe/main.nf
index 21c93c1c..5952f9a7 100644
--- a/nextflow-modules/modules/mykrobe/main.nf
+++ b/nextflow-modules/modules/mykrobe/main.nf
@@ -10,7 +10,7 @@ process mykrobe {
     path "*versions.yml"              , emit: versions
 
   when:
-    workflow.profile == "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     def args = task.ext.args ?: ''
diff --git a/nextflow-modules/modules/prp/main.nf b/nextflow-modules/modules/prp/main.nf
index 88f86aea..250bceb4 100644
--- 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)
+    tuple val(sample_id), path(bam), val(platform)
     path reference
     path bed
 
@@ -125,7 +125,7 @@ process post_align_qc {
     tuple val(sample_id), path(output), emit: qc
 
   when:
-    workflow.profile != "streptococcus"
+    task.ext.when && platform == "illumina"
 
   script:
     output = "${sample_id}_qc.json"
@@ -153,7 +153,7 @@ process annotate_delly {
     tuple val(sample_id), path(output), emit: vcf
 
   when:
-    workflow.profile == "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     output = "${sample_id}_annotated_delly.vcf"
@@ -180,6 +180,9 @@ process add_igv_track {
   output:
     tuple val(sample_id), path(output), emit: json
 
+  when:
+    task.ext.when
+
   script:
     output = "${sample_id}_result.json"
     """
diff --git a/nextflow-modules/modules/resfinder/main.nf b/nextflow-modules/modules/resfinder/main.nf
index b972f511..230ad995 100644
--- a/nextflow-modules/modules/resfinder/main.nf
+++ b/nextflow-modules/modules/resfinder/main.nf
@@ -17,6 +17,9 @@ process resfinder {
     path output_point                      , optional: true, emit: point_table
     path "*versions.yml"                   , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     def resfinder_arg = resfinder_db ? "--acquired --db_path_res ${resfinder_db}" : ""
     def pointfinder_arg = pointfinder_db ? "--point --db_path_point ${pointfinder_db}" : ""
diff --git a/nextflow-modules/modules/samtools/main.nf b/nextflow-modules/modules/samtools/main.nf
index 8acd6032..b7146c96 100644
--- a/nextflow-modules/modules/samtools/main.nf
+++ b/nextflow-modules/modules/samtools/main.nf
@@ -12,7 +12,7 @@ process samtools_view {
     path "*versions.yml"          , emit: versions
   
   when:
-    workflow.profile != "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     def reference_arg = fasta ? "--reference ${fasta} -C" : ""
@@ -91,6 +91,9 @@ process samtools_index {
     tuple val(sample_id), path(output), emit: bai
     path "*versions.yml"              , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     output = "${input}.bai"
     """
diff --git a/nextflow-modules/modules/sccmec/main.nf b/nextflow-modules/modules/sccmec/main.nf
index f87ea6dc..3b103c03 100644
--- a/nextflow-modules/modules/sccmec/main.nf
+++ b/nextflow-modules/modules/sccmec/main.nf
@@ -9,6 +9,9 @@ process sccmec {
     tuple val(sample_id), path(output), emit: tsv 
     path "*versions.yml"              , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     def args = task.ext.args ?: ''
     output = "${sample_id}_sccmec.tsv"
@@ -20,7 +23,7 @@ process sccmec {
     cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
     ${task.process}:
      sccmec:
-      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p' | sed 's/ .*//')
       container: ${task.container}
     END_VERSIONS
     """
@@ -33,7 +36,7 @@ process sccmec {
     cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
     ${task.process}:
      sccmec:
-      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p')
+      version: \$(echo \$(sccmec --version 2>&1) | sed -n 's/.*sccmec_targets, version //p' | sed 's/ .*//')
       container: ${task.container}
     END_VERSIONS
     """
diff --git a/nextflow-modules/modules/serotypefinder/main.nf b/nextflow-modules/modules/serotypefinder/main.nf
index 6a4fcf90..025d51a2 100644
--- a/nextflow-modules/modules/serotypefinder/main.nf
+++ b/nextflow-modules/modules/serotypefinder/main.nf
@@ -13,7 +13,7 @@ process serotypefinder {
     path "*versions.yml"                   , emit: versions
 
   when:
-    !(workflow.profile in ["mycobacterium_tuberculosis", "staphylococcus_aureus", "streptococcus", "streptococcus_pyogenes"])
+    task.ext.when
 
   script:
     databases_arg = databases ? "--databases ${databases.join(',')}" : ""
diff --git a/nextflow-modules/modules/shigapass/main.nf b/nextflow-modules/modules/shigapass/main.nf
index bc421c31..bdbeb8e9 100644
--- a/nextflow-modules/modules/shigapass/main.nf
+++ b/nextflow-modules/modules/shigapass/main.nf
@@ -11,7 +11,7 @@ process shigapass {
     path "*versions.yml"              , emit: versions
 
   when:
-    workflow.profile == "escherichia_coli"
+    task.ext.when
 
   script:
     shigapass_db_arg = shigapass_db ? "-p ${shigapass_db}" : "-p /usr/local/share/shigapass-1.5.0/db/"
diff --git a/nextflow-modules/modules/snippy/main.nf b/nextflow-modules/modules/snippy/main.nf
index 1f13a821..82a0c08c 100644
--- a/nextflow-modules/modules/snippy/main.nf
+++ b/nextflow-modules/modules/snippy/main.nf
@@ -13,7 +13,7 @@ process snippy {
     path "*versions.yml"                               , emit: versions
 
   when:
-    workflow.profile == "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     def args = task.ext.args ?: ''
@@ -42,7 +42,7 @@ process snippy {
     """
     mkdir ${sample_id}
     touch ${output}
-    touch "${sample_id}/snps.{vcf,bed,gff,csv,tab,html,bam,txt}"
+    touch ${sample_id}/snps.{vcf,bed,gff,csv,tab,html,bam,txt}
 
     cat <<-END_VERSIONS > ${sample_id}_${task.process}_versions.yml
     ${task.process}:
diff --git a/nextflow-modules/modules/tbprofiler/main.nf b/nextflow-modules/modules/tbprofiler/main.nf
index 3357f08f..c57c00f4 100644
--- a/nextflow-modules/modules/tbprofiler/main.nf
+++ b/nextflow-modules/modules/tbprofiler/main.nf
@@ -13,7 +13,7 @@ process tbprofiler {
     path "*versions.yml"                   , emit: versions
 
   when:
-    workflow.profile == "mycobacterium_tuberculosis"
+    task.ext.when
 
   script:
     def args = task.ext.args ?: ''
diff --git a/nextflow-modules/modules/virulencefinder/main.nf b/nextflow-modules/modules/virulencefinder/main.nf
index 525f0fa0..be57ea88 100644
--- a/nextflow-modules/modules/virulencefinder/main.nf
+++ b/nextflow-modules/modules/virulencefinder/main.nf
@@ -12,6 +12,9 @@ process virulencefinder {
     tuple val(sample_id), path(meta_output), emit: meta
     path "*versions.yml"                   , emit: versions
 
+  when:
+    task.ext.when
+
   script:
     databases_arg = databases ? "--databases ${databases.join(',')}" : ""
     output = "${sample_id}_virulencefinder.json"
diff --git a/workflows/bacterial_base.nf b/workflows/bacterial_base.nf
index 9b293493..b5c23a16 100644
--- a/workflows/bacterial_base.nf
+++ b/workflows/bacterial_base.nf
@@ -97,11 +97,11 @@ workflow CALL_BACTERIAL_BASE {
         quast(ch_assembly, referenceGenome)
 
         // qc processing
-        fastqc(ch_reads)
+        fastqc(ch_reads_w_meta)
         bwa_mem_ref(ch_reads, referenceGenomeDir)
         samtools_index_ref(bwa_mem_ref.out.bam)
 
-        post_align_qc(bwa_mem_ref.out.bam, referenceGenome, coreLociBed)
+        post_align_qc(bwa_mem_ref.out.bam.join(ch_meta), referenceGenome, coreLociBed)
 
         nanoplot(ch_reads_w_meta)
 
@@ -127,6 +127,7 @@ workflow CALL_BACTERIAL_BASE {
         bam             = bwa_mem_ref.out.bam               // channel: [ val(meta), path(bam)]
         bai             = samtools_index_ref.out.bai        // channel: [ val(meta), path(bai)]
         fastqc          = fastqc.out.output                 // channel: [ val(meta), path(txt)]
+        seqplat_meta    = ch_meta                           // channel: [ val(meta), val(str)]
         metadata        = save_analysis_metadata.out.meta   // channel: [ val(meta), path(json)]
         qc              = post_align_qc.out.qc              // channel: [ val(meta), path(fasta)]
         qc_nano         = nanoplot.out.html                 // channel: [ val(meta), path(html)]
diff --git a/workflows/escherichia_coli.nf b/workflows/escherichia_coli.nf
index ff240219..955320ea 100644
--- a/workflows/escherichia_coli.nf
+++ b/workflows/escherichia_coli.nf
@@ -60,6 +60,7 @@ workflow CALL_ESCHERICHIA_COLI {
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.qc.set{ch_qc}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -118,8 +119,10 @@ workflow CALL_ESCHERICHIA_COLI {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
+        ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
@@ -155,7 +158,7 @@ workflow CALL_ESCHERICHIA_COLI {
         create_yaml(create_analysis_result.out.json.join(ch_sourmash).join(ch_ska), params.speciesDir)
 
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(chewbbaca_split_results.out.output)
             .set{ cdmInput }
 
diff --git a/workflows/klebsiella_pneumoniae.nf b/workflows/klebsiella_pneumoniae.nf
index bd19746b..401cff52 100644
--- a/workflows/klebsiella_pneumoniae.nf
+++ b/workflows/klebsiella_pneumoniae.nf
@@ -58,6 +58,7 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.qc.set{ch_qc}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -115,8 +116,10 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
+        ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
@@ -152,7 +155,7 @@ workflow CALL_KLEBSIELLA_PNEUMONIAE {
         create_yaml(create_analysis_result.out.json.join(ch_sourmash).join(ch_ska), params.speciesDir)
 
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(chewbbaca_split_results.out.output)
             .set{ cdmInput }
 
diff --git a/workflows/mycobacterium_tuberculosis.nf b/workflows/mycobacterium_tuberculosis.nf
index f0633c7c..dbcfd5f0 100644
--- a/workflows/mycobacterium_tuberculosis.nf
+++ b/workflows/mycobacterium_tuberculosis.nf
@@ -45,6 +45,7 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
         CALL_BACTERIAL_BASE.out.reads.set{ch_reads}
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -63,8 +64,10 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
+        ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(ch_empty)
             .join(ch_empty)
             .join(ch_empty)
@@ -105,7 +108,7 @@ workflow CALL_MYCOBACTERIUM_TUBERCULOSIS {
         create_yaml(add_grading_bed_track.out.json.join(ch_sourmash).join(ch_ska), params.speciesDir)
 
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(ch_empty)
             .set{ cdmInput }
 
diff --git a/workflows/staphylococcus_aureus.nf b/workflows/staphylococcus_aureus.nf
index f42d14c3..5fe24754 100644
--- a/workflows/staphylococcus_aureus.nf
+++ b/workflows/staphylococcus_aureus.nf
@@ -57,6 +57,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.qc.set{ch_qc}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -114,8 +115,10 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
+        ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
@@ -151,7 +154,7 @@ workflow CALL_STAPHYLOCOCCUS_AUREUS {
         create_yaml(create_analysis_result.out.json.join(ch_sourmash).join(ch_ska), params.speciesDir)
 
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(chewbbaca_split_results.out.output)
             .set{ cdmInput }
 
diff --git a/workflows/streptococcus.nf b/workflows/streptococcus.nf
index cda53985..673b401c 100644
--- a/workflows/streptococcus.nf
+++ b/workflows/streptococcus.nf
@@ -67,6 +67,7 @@ workflow CALL_STREPTOCOCCUS {
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.qc.set{ch_qc}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -125,9 +126,15 @@ workflow CALL_STREPTOCOCCUS {
         virulencefinder(ch_reads, params.useVirulenceDbs, virulencefinderDb)
 
         ch_reads.map{ sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
+        
+        if (species == "streptococcus") {
+            ch_empty.set{ ch_qc_illumina }
+        } else {
+            ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+        }
 
         ch_quast
-            .join(ch_empty)
+            .join(ch_qc_illumina)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
@@ -163,7 +170,7 @@ workflow CALL_STREPTOCOCCUS {
         create_yaml(create_analysis_result.out.json.join(ch_sourmash).join(ch_ska), speciesDir)
 
         ch_quast
-            .join(ch_empty)
+            .join(ch_qc_illumina)
             .join(chewbbaca_split_results.out.output)
             .set{ cdmInput }
 
diff --git a/workflows/streptococcus_pyogenes.nf b/workflows/streptococcus_pyogenes.nf
index 025ab3d8..040f7599 100644
--- a/workflows/streptococcus_pyogenes.nf
+++ b/workflows/streptococcus_pyogenes.nf
@@ -61,6 +61,7 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
         CALL_BACTERIAL_BASE.out.quast.set{ch_quast}
         CALL_BACTERIAL_BASE.out.qc.set{ch_qc}
         CALL_BACTERIAL_BASE.out.metadata.set{ch_metadata}
+        CALL_BACTERIAL_BASE.out.seqplat_meta.set{ch_seqplat_meta}
         CALL_BACTERIAL_BASE.out.seqrun_meta.set{ch_seqrun_meta}
         CALL_BACTERIAL_BASE.out.reads_w_meta.set{ch_input_meta}
         CALL_BACTERIAL_BASE.out.sourmash.set{ch_sourmash}
@@ -118,8 +119,10 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
 
         ch_reads.map { sampleID, reads -> [ sampleID, [] ] }.set{ ch_empty }
 
+        ch_qc_illumina = ch_seqplat_meta.filter { it[1] == 'illumina' } ? ch_qc : ch_empty
+
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(mlst.out.json)
             .join(chewbbaca_split_results.out.output)
             .join(amrfinderplus.out.output)
@@ -155,7 +158,7 @@ workflow CALL_STREPTOCOCCUS_PYOGENES {
         create_yaml(create_analysis_result.out.json.join(ch_sourmash).join(ch_ska), speciesDir)
 
         ch_quast
-            .join(ch_qc)
+            .join(ch_qc_illumina)
             .join(chewbbaca_split_results.out.output)
             .set{ cdmInput }