Merge pull request #371 from genomic-medicine-sweden/370-fix-channel-…

…of-bug Fix channel of bug
genomic-medicine-sweden · Nov 13, 2024 · 999b2bd · 999b2bd
2 parents 516219d + c871044
commit 999b2bd
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Showing 13 changed files with 94 additions and 117 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Fixed `nextflow.hopper.config` `symlinkDir`
 - 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([])`
 
 ### Changed
 

diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -5,6 +5,7 @@ params {
 	pointfinderDb = "${root}/assets/pointfinder_db"
 	serotypefinderDb = "${root}/assets/serotypefinder_db"
 	virulencefinderDb = "${root}/assets/virulencefinder_db"
+	mlstBlastDb = "${root}/assets/mlst_db/blast"
 	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
 	krakenDb = "/filepath/to/kraken_db" //edit if useKraken = true
 	workDir = "/filepath/to/workdir" //edit
@@ -32,7 +33,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -51,7 +51,6 @@ profiles {
 		// 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 = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases"
@@ -68,7 +67,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -99,7 +97,6 @@ profiles {
 		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 = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
@@ -115,7 +112,6 @@ profiles {
 		params.referenceGenome = null
 		params.referenceGenomeIdx = null
 		params.referenceGenomeGff = null
-		params.mlstBlastDb = null
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
 		params.shigapassDb = null
 		params.coreLociBed = null

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -5,6 +5,7 @@ params {
 	pointfinderDb = "${root}/assets/pointfinder_db"
 	serotypefinderDb = "${root}/assets/serotypefinder_db"
 	virulencefinderDb = "${root}/assets/virulencefinder_db"
+	mlstBlastDb = "${root}/assets/mlst_db/blast"
 	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
 	krakenDb = "/tmp/jsn" //edit if useKraken = true
 	workDir = "/tmp/jsn" //edit
@@ -36,7 +37,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -55,7 +55,6 @@ profiles {
 		// 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 = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases"
@@ -72,7 +71,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -103,7 +101,6 @@ profiles {
 		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 = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
@@ -119,7 +116,6 @@ profiles {
 		params.referenceGenome = null
 		params.referenceGenomeIdx = null
 		params.referenceGenomeGff = null
-		params.mlstBlastDb = null
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
 		params.shigapassDb = null
 		params.coreLociBed = null

diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
@@ -8,6 +8,7 @@ params {
 	pointfinderDb = "${root}/assets/pointfinder_db"
 	serotypefinderDb = "${root}/assets/serotypefinder_db"
 	virulencefinderDb = "${root}/assets/virulencefinder_db"
+	mlstBlastDb = "${root}/assets/mlst_db/blast"
 	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
 	krakenDb = "/fs1/resources/ref/micro/krakenstd"
 	// INPUT & OUTPUT //
@@ -45,7 +46,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -65,7 +65,6 @@ profiles {
 		// 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 = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${params.root}/assets/wgmlst/escherichia_coli/alleles/ecoli_INNUENDO_wgMLST"
 		params.shigapassDb = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases"
 		params.coreLociBed = "${params.root}/assets/wgmlst/escherichia_coli/bed/GCF_000005845.2.bed"
@@ -83,7 +82,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -115,7 +113,6 @@ profiles {
 		params.referenceGenome = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.fasta"
 		params.referenceGenomeIdx = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.fasta.fai"
 		params.referenceGenomeGff = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_000006785.2.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed"
 		params.coreLociBed = "${params.root}/assets/cgmlst/streptococcus_pyogenes/bed/GCF_000006785.2.bed"
 		params.trainingFile = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
@@ -131,7 +128,6 @@ profiles {
 		params.referenceGenome = null
 		params.referenceGenomeIdx = null
 		params.referenceGenomeGff = null
-		params.mlstBlastDb = null
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
 		params.shigapassDb = null
 		params.coreLociBed = null

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -8,6 +8,7 @@ params {
 	pointfinderDb = "${root}/assets/pointfinder_db"
 	serotypefinderDb = "${root}/assets/serotypefinder_db"
 	virulencefinderDb = "${root}/assets/virulencefinder_db"
+	mlstBlastDb = "${root}/assets/mlst_db/blast"
 	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
 	krakenDb = "/fs1/resources/ref/micro/krakenstd"
 	// INPUT & OUTPUT //
@@ -44,7 +45,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -64,7 +64,6 @@ profiles {
 		// 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 = "${params.root}/assets/cgmlst/escherichia_coli/alleles_rereffed/Escherichia_coli.trn"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/ShigaPass/SCRIPT/ShigaPass_DataBases"
@@ -82,7 +81,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -115,7 +113,6 @@ profiles {
 		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 = "${params.root}/assets/genomes/streptococcus_pyogenes/GCF_900475035.1.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/cgmlst/streptococcus_pyogenes/alleles_rereffed/Streptococcus_pyogenes.trn"
@@ -131,7 +128,6 @@ profiles {
 		params.referenceGenome = null
 		params.referenceGenomeIdx = null
 		params.referenceGenomeGff = null
-		params.mlstBlastDb = null
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
 		params.shigapassDb = null
 		params.coreLociBed = null

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -2,10 +2,11 @@ params {
 	penv = "OpenMP"
 	root = "/gms-apps/pipelines/jasen" //edit
 	amrfinderDb = "${root}/assets/amrfinder_db/latest"
-	resfinderDb = "${params.root}/assets/resfinder_db"
-	pointfinderDb = "${params.root}/assets/pointfinder_db"
+	resfinderDb = "${root}/assets/resfinder_db"
+	pointfinderDb = "${root}/assets/pointfinder_db"
 	serotypefinderDb = "${root}/assets/serotypefinder_db"
-	virulencefinderDb = "${params.root}/assets/virulencefinder_db"
+	virulencefinderDb = "${root}/assets/virulencefinder_db"
+	mlstBlastDb = "${root}/assets/mlst_db/blast"
 	pubMlstDb = "${root}/assets/mlst_db/pubmlst"
 	krakenDb = "/gms-home/isasyl/code/JASEN" //edit if useKraken = true
 	workDir = "/gms-apps/pipelines/jasen/trash" //edit
@@ -58,7 +59,6 @@ profiles {
 		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 = "${params.root}/assets/genomes/staphylococcus_aureus/GCF_000012045.1.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/prodigal_training_files/Staphylococcus_aureus.trn"
@@ -77,7 +77,6 @@ profiles {
 		// params.chewbbacaDb = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -94,7 +93,6 @@ profiles {
 		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 = "${params.root}/assets/genomes/klebsiella_pneumoniae/GCF_000240185.1.gff"
-		params.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		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 = "${params.root}/assets/cgmlst/klebsiella_pneumoniae/alleles_rereffed/Klebsiella_pneumoniae.trn"
@@ -125,7 +123,6 @@ profiles {
 		params.referenceGenome = "${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.mlstBlastDb = "${params.root}/assets/mlst_db/blast"
 		params.chewbbacaDb = "${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"
@@ -141,7 +138,6 @@ profiles {
 		params.referenceGenome = null
 		params.referenceGenomeIdx = null
 		params.referenceGenomeGff = null
-		params.mlstBlastDb = null
 		params.chewbbacaDb = "${params.root}/assets/cgmlst/streptococcus/alleles_rereffed"
 		params.shigapassDb = null
 		params.coreLociBed = null