Merge pull request genomic-medicine-sweden#333 from genomic-medicine-…

…sweden/332-fix-cdm-input-bug 332 fix cdm input bug
Genomic-Medicine-Linkoping · Aug 9, 2024 · f28fd4d · f28fd4d
2 parents 3efb3af + 0356809
commit f28fd4d
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Showing 7 changed files with 15 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,8 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- Added `cdmDir` to config
+
 ### Fixed
 
+- Fixed `--qc` argument filepath to be full filepath to output
+
 ### Changed
 
 - Updated TbProfiler to version 6.3

diff --git a/configs/nextflow.base.config b/configs/nextflow.base.config
@@ -17,6 +17,7 @@ params {
 	args = ""
 	prefix = ""
 	bamDir = "bam"
+	cdmDir = "cdm_input"
 	vcfDir = "vcf"
 	cronCopy = false
 	useKraken = true
@@ -161,7 +162,7 @@ process {
 	}
 	withName: create_cdm_input {
 		container = "${params.containerDir}/bonsai-prp.sif"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "${params.containerDir}/bonsai-prp.sif"

diff --git a/configs/nextflow.ci.config b/configs/nextflow.ci.config
@@ -17,6 +17,7 @@ params {
 	args = ""
 	prefix = ""
 	bamDir = "bam"
+	cdmDir = "cdm_input"
 	vcfDir = "vcf"
 	cronCopy = false
 	useKraken = false
@@ -150,7 +151,7 @@ process {
 	}
 	withName: create_cdm_input {
 		container = "${params.containerDir}/bonsai-prp.sif"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "${params.containerDir}/bonsai-prp.sif"

diff --git a/configs/nextflow.dev.config b/configs/nextflow.dev.config
@@ -21,6 +21,7 @@ params {
 	args = ""
 	prefix = ""
 	bamDir = "bam"
+	cdmDir = "cdm_input"
 	vcfDir = "vcf"
 	// PIPELINE OPTIONS //
 	devMode = true
@@ -165,7 +166,7 @@ process {
 	}
 	withName: create_cdm_input {
 		container = "${params.containerDir}/bonsai-prp.sif"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "${params.containerDir}/bonsai-prp.sif"

diff --git a/configs/nextflow.hopper.config b/configs/nextflow.hopper.config
@@ -21,6 +21,7 @@ params {
 	args = ""
 	prefix = ""
 	bamDir = "bam"
+	cdmDir = "cdm_input"
 	vcfDir = "vcf"
 	// PIPELINE OPTIONS //
 	cronCopy = true
@@ -164,7 +165,7 @@ process {
 	}
 	withName: create_cdm_input {
 		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"

diff --git a/configs/nextflow.ngp.config b/configs/nextflow.ngp.config
@@ -18,6 +18,7 @@ params {
 	args = ""
 	prefix = ""
 	bamDir = "bam"
+	cdmDir = "cdm_input"
 	vcfDir = "vcf"
 	cronCopy = false
 	useKraken = false
@@ -174,7 +175,7 @@ process {
 	}
 	withName: create_cdm_input {
 		container = "${params.containerDir}/bonsai-prp.sif"
-		publishDir = [ path: "${params.outdir}/${params.speciesDir}/cdm_input", mode: 'copy', overwrite: true ]
+		publishDir = [ path: "${params.outdir}/${params.speciesDir}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "${params.containerDir}/bonsai-prp.sif"

diff --git a/nextflow-modules/modules/cmd/main.nf b/nextflow-modules/modules/cmd/main.nf
@@ -17,7 +17,7 @@ process export_to_cdm {
     echo ${sequencingRun} \\
          --sample-id ${sampleName} \\
          --assay ${species} \\
-         --qc ${qc} \\
+         --qc ${params.outdir}/${params.speciesDir}/${params.cdmDir}/${qc} \\
          ${limsID} > ${output}
     """