Merge pull request #31 from UMCUGenetics/develop

v1.3.0
UMCUGenetics · Apr 22, 2021 · e834db8 · e834db8
2 parents 607e121 + 91574ad
commit e834db8
Show file tree

Hide file tree

Showing 5 changed files with 64 additions and 12 deletions.
diff --git a/NextflowModules b/NextflowModules
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
-# DxNextflowWES
+# DxNextflowWES [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4551799.svg)](https://doi.org/10.5281/zenodo.4551799)
+
 Genome Diagnostics Nextflow WES workflow
 
 #### Get Nextflow Modules

diff --git a/WES.config b/WES.config
@@ -153,7 +153,7 @@ process {
         cpus = 2
         memory = '20G'
         time = '2h'
-      
+
         publishDir = [
             [path: "$params.outdir/exomedepth/UMCU", mode: 'copy', pattern: 'UMCU*.vcf'],
             [path: "$params.outdir/exomedepth/HC", mode: 'copy', pattern: 'HC*.vcf'],
@@ -232,7 +232,7 @@ process {
         }
     }
 
-    withLabel: MultiQC_1_8 {
+    withLabel: MultiQC_1_10 {
         cpus = 2
         memory = '1G'
         time = '5m'
@@ -270,7 +270,7 @@ process {
         memory = '5G'
         time = '1h'
     }
- 
+
     withLabel: SavePedFile {
         cpus = 2
         memory = '1G'
@@ -280,7 +280,7 @@ process {
             path = "$params.outdir/QC/Kinship"
             mode = 'copy'
         }
-    }    
+    }
 
     withLabel: VersionLog {
         cpus = 2

diff --git a/WES.nf b/WES.nf
@@ -31,7 +31,7 @@ include CollectMultipleMetrics as PICARD_CollectMultipleMetrics from './Nextflow
 include EstimateLibraryComplexity as PICARD_EstimateLibraryComplexity from './NextflowModules/Picard/2.22.0/EstimateLibraryComplexity.nf' params(optional:"OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500")
 include CollectHsMetrics as PICARD_CollectHsMetrics from './NextflowModules/Picard/2.22.0/CollectHsMetrics.nf' params(genome:"$params.genome", bait:"$params.dxtracks_path/$params.picard_bait", target:"$params.dxtracks_path/$params.picard_target", optional: "METRIC_ACCUMULATION_LEVEL=null METRIC_ACCUMULATION_LEVEL=SAMPLE")
 include Flagstat as Sambamba_Flagstat from './NextflowModules/Sambamba/0.7.0/Flagstat.nf'
-include MultiQC from './NextflowModules/MultiQC/1.8/MultiQC.nf' params(optional:"--config $baseDir/assets/multiqc_config.yaml")
+include MultiQC from './NextflowModules/MultiQC/1.10/MultiQC.nf' params(optional:"--config $baseDir/assets/multiqc_config.yaml")
 
 def fastq_files = extractFastqPairFromDir(params.fastq_path)
 def analysis_id = params.outdir.split('/')[-1]
@@ -148,7 +148,7 @@ process ExonCov {
     script:
         """
         source ${params.exoncov_path}/venv/bin/activate
-        python ${params.exoncov_path}/ExonCov.py import_bam --threads ${task.cpus} --overwrite --exon_bed ${params.dxtracks_path}/${params.exoncov_bed} ${analysis_id} ${bam_file}
+        python ${params.exoncov_path}/ExonCov.py import_bam --threads ${task.cpus} --overwrite --exon_bed ${params.dxtracks_path}/${params.exoncov_bed} ${analysis_id} WES ${bam_file}
         """
 }
 
@@ -174,7 +174,7 @@ process ExomeDepth {
     script:
         """
         source ${params.exomedepth_path}/venv/bin/activate
-        python ${params.exomedepth_path}/run_ExomeDepth.py callcnv ./ ${bam_file} ${analysis_id} ${sample_id} 
+        python ${params.exomedepth_path}/run_ExomeDepth.py callcnv ./ ${bam_file} ${analysis_id} ${sample_id}
         """
 }
 
@@ -281,6 +281,7 @@ process SavePedFile {
     tag {"SavePedFile ${analysis_id}"}
     label 'SavePedFile'
     shell = ['/bin/bash', '-euo', 'pipefail']
+    cache = false  //Disable cache to force a new ped file copy when restarting the workflow.
 
     output:
         path("*.ped")
@@ -296,6 +297,7 @@ process VersionLog {
     tag {"VersionLog ${analysis_id}"}
     label 'VersionLog'
     shell = ['/bin/bash', '-eo', 'pipefail']
+    cache = false  //Disable cache to force a new version log when restarting the workflow.
 
     output:
         path('repository_version.log')

diff --git a/assets/multiqc_config.yaml b/assets/multiqc_config.yaml
@@ -1,11 +1,10 @@
 extra_fn_clean_exts:
-    - type: regex
-      pattern: '_\w*_S\d+_L\d{3}_R\d_\d{3}'
     - '.LibraryComplexity'
 
 top_modules:
-- 'fastqc'
 - 'picard'
+- 'fastqc'
+
 
 picard_config:
     general_stats_target_coverage:
@@ -16,6 +15,56 @@ picard_config:
         - 40
         - 50
         - 100
+    HsMetrics_table_cols:
+        - AT_DROPOUT
+        - BAIT_DESIGN_EFFICIENCY
+        - BAIT_TERRITORY
+        - FOLD_80_BASE_PENALTY
+        - FOLD_ENRICHMENT
+        - GC_DROPOUT
+        - HET_SNP_Q
+        - HET_SNP_SENSITIVITY
+        - MAX_TARGET_COVERAGE
+        - MEAN_BAIT_COVERAGE
+        - MEAN_TARGET_COVERAGE
+        - MEDIAN_TARGET_COVERAGE
+        - NEAR_BAIT_BASES
+        - OFF_BAIT_BASES
+        - ON_BAIT_BASES
+        - ON_BAIT_VS_SELECTED
+        - ON_TARGET_BASES
+        - PCT_SELECTED_BASES
+        - PCT_USABLE_BASES_ON_BAIT
+        - PCT_USABLE_BASES_ON_TARGET
+        - PF_BASES_ALIGNED
+        - PF_READS
+        - PF_UNIQUE_READS
+        - PF_UQ_BASES_ALIGNED
+        - PF_UQ_READS_ALIGNED
+        - TARGET_TERRITORY
+        - TOTAL_READS
+        - ZERO_CVG_TARGETS_PCT
+    HsMetrics_table_cols_hidden:
+        - BAIT_DESIGN_EFFICIENCY
+        - BAIT_TERRITORY
+        - FOLD_ENRICHMENT
+        - HET_SNP_Q
+        - HET_SNP_SENSITIVITY
+        - MAX_TARGET_COVERAGE
+        - MEDIAN_TARGET_COVERAGE
+        - NEAR_BAIT_BASES
+        - OFF_BAIT_BASES
+        - ON_BAIT_BASES
+        - ON_BAIT_VS_SELECTED
+        - ON_TARGET_BASES
+        - PF_BASES_ALIGNED
+        - PF_READS
+        - PF_UNIQUE_READS
+        - PF_UQ_BASES_ALIGNED
+        - PF_UQ_READS_ALIGNED
+        - TARGET_TERRITORY
+        - ZERO_CVG_TARGETS_PCT
+
 
 table_columns_visible:
     FastQC:
+2 −4		BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
+18 −0		MultiQC/1.10/MultiQC.nf
+2 −1		README.md
+0 −1		RSeQC/3.0.1/RSeQC.nf
+2 −8		STAR/2.7.3a/AlignReads.nf
+4 −4		Salmon/1.2.1/QuantMerge.nf
+3 −2		Subread/2.0.0/FeatureCounts.nf
+9 −10		Utils/MergeFastqLanes.nf