Merge branch 'master' into 297-add-nanopore-test-data

genomic-medicine-sweden · Aug 12, 2024 · f27dcef · f27dcef
2 parents 101715c + f28fd4d
commit f27dcef
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Showing 8 changed files with 21 additions and 10 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,13 +8,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+
 - Added long-read test data (S. aureus)
 - Added `samplelist_nanopore.csv` for running long-read test data
 - Added location of documentation to `README` 
+- Added `cdmDir` to config
+
 ### Fixed
 
+- Fixed `--qc` argument filepath to be full filepath to output
+
 ### Changed
 
+- Updated TbProfiler to version 6.3
+
 ## [0.8.0]
 
 ### Added

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 = "${params.containerDir}/bonsai-prp.sif"
@@ -275,7 +276,7 @@ process {
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12 GB'
-		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.2.0--pyhdfd78af_1"
+		container = "https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0"
 		publishDir = [ [ path: "${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'"
 	}

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}/${params.cdmDir}", mode: 'copy', overwrite: true ]
 	}
 	withName: create_yaml {
 		container = "docker://clinicalgenomicslund/bonsai-prp:0.9.3"
@@ -290,7 +291,7 @@ process {
 	withName: tbprofiler_mergedb {
 		cpus = 16
 		memory = '12 GB'
-		container = "https://depot.galaxyproject.org/singularity/tb-profiler:6.2.0--pyhdfd78af_1"
+		container = "https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0"
 		publishDir = [ [ path: "${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'"
 	}

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/container/Makefile b/container/Makefile
@@ -66,7 +66,7 @@ URL_skesa := https://depot.galaxyproject.org/singularity/skesa:2.5.1--hdcf5f25_0
 URL_snippy := https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2
 URL_sourmash := https://depot.galaxyproject.org/singularity/sourmash:4.8.2--hdfd78af_0
 URL_spades := https://depot.galaxyproject.org/singularity/spades:3.15.5--h95f258a_1
-URL_tb-profiler := https://depot.galaxyproject.org/singularity/tb-profiler:6.2.0--pyhdfd78af_0
+URL_tb-profiler := https://depot.galaxyproject.org/singularity/tb-profiler%3A6.3.0--pyhdfd78af_0
 URL_virulencefinder := https://depot.galaxyproject.org/singularity/virulencefinder:2.0.4--hdfd78af_1
 
 define log_message
@@ -113,4 +113,3 @@ $(local_containers):
 	&& output_file=$$(echo ${container_url} | sed -e 's#docker://##' -e 's#/#-#g' -e 's#:#-#g').img \
 	&& sudo singularity build --force $${output_file} ${container_url} \
 	&& ln -sf $${output_file} $@ 
-
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}
     """