Merge pull request #19 from UMCUGenetics/release/v2.0.0

Release/v2.0.0
UMCUGenetics · Jul 6, 2023 · 97cb9cd · 97cb9cd
2 parents b8d9088 + 240cc44
commit 97cb9cd
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Showing 5 changed files with 14 additions and 8 deletions.
diff --git a/NextflowModules b/NextflowModules
diff --git a/README.md b/README.md
@@ -1,4 +1,5 @@
-# DxNextflowWGS
+# DxNextflowWGS [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4709755.svg)](https://doi.org/10.5281/zenodo.4709755)
+
 Genome Diagnostics Nextflow WGS workflow
 
 ## Get Nextflow Modules
@@ -33,4 +34,4 @@ cp /guix/path.gz.squashfs baf_nextflow.gz.squashfs
 unsquashfs baf_nextflow.gz.squashfs
 chmod -R 0775 squashfs-root
 singularity build baf_nextflow.sif squashfs-root
-```
+```
diff --git a/WGS.config b/WGS.config
@@ -2,7 +2,7 @@ params {
     genome = '/hpc/diaggen/data/databases/ref_genomes/Homo_sapiens.GRCh37.GATK.illumina/Homo_sapiens.GRCh37.GATK.illumina.fasta'
     dxtracks_path = '/hpc/diaggen/software/production/Dx_tracks'
 
-    gatk_path = '/hpc/local/CentOS7/cog_bioinf/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar'
+    gatk_path = '/hpc/diaggen/software/tools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef/GenomeAnalysisTK.jar'
     gatk_bqsr_options = '--knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf.gz --knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/dbsnp_137.b37.vcf.gz --knownSites /hpc/diaggen/data/databases/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.gz'
     gatk_bqsr_pr_options = '--static_quantized_quals 10 --static_quantized_quals 20 --static_quantized_quals 30'
     fingerprint_target = 'fingerprint/81SNP_design.vcf'
@@ -155,7 +155,7 @@ process {
         }
     }
 
-    withLabel: ControlFreec_11_5_makeGraph {
+    withLabel: ControlFreec_11_5_MakeGraph {
         cpus = 4
         memory = { 5.GB * task.attempt }
         time = { (1.s * cnv_file.size() / 140) * task.attempt }

diff --git a/WGS.nf b/WGS.nf
@@ -219,7 +219,7 @@ process GetStatsFromFlagstat {
 
     script:
         """
-        python ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
+        python2 ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
         """
 }
 

diff --git a/run_nextflow_wgs.sh b/run_nextflow_wgs.sh
@@ -28,8 +28,6 @@ sbatch <<EOT
 #SBATCH --export=NONE
 #SBATCH --account=diaggen
 
-module load Java/1.8.0_60
-
 /hpc/diaggen/software/tools/nextflow run $workflow_path/WGS.nf \
 -c $workflow_path/WGS.config \
 --fastq_path $input \
@@ -55,11 +53,18 @@ if [ \$? -eq 0 ]; then
     rm workflow.running
     touch workflow.done
 
+    echo "Change permissions"
+    chmod 775 -R $output
+    
     exit 0
 else
     echo "Nextflow failed"
     rm workflow.running
     touch workflow.failed
+    
+    echo "Change permissions"
+    chmod 775 -R $output
+    
     exit 1
 fi
 EOT
+1 −1		BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf
+1 −1		ControlFREEC/11.5/AssessSignificance.nf
+1 −2		ControlFREEC/11.5/Freec.nf
+1 −1		ControlFREEC/11.5/MakeGraph.nf
+1 −1		ControlFREEC/11.5/MakeKaryotype.nf
+63 −0		GATK/4.2.1.0/GenotypeGvcfs.nf
+65 −0		GATK/4.2.1.0/HaplotypeCaller.nf
+44 −0		GATK/4.2.1.0/MergeVcfs.nf
+30 −0		GATK/4.2.1.0/SelectVariants.nf
+48 −0		GATK/4.2.1.0/VariantFiltration.nf
+19 −0		Mosdepth/0.3.3/Mosdepth.nf
+18 −0		Sambamba/0.7.0/ViewSubsample.nf
+1 −1		SortMeRNA/4.2.0/SortMeRNA.nf
+1 −1		SortMeRNA/4.3.3/SortMeRNA.nf
-Original file line number
+Diff line change
@@ Expand Up / @@ -219,7 +219,7 @@ process GetStatsFromFlagstat { @@
         script:
             """
-            python ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
+            python2 ${baseDir}/assets/get_stats_from_flagstat.py ${flagstat_files} > run_stats.txt
             """
     }
@@ Expand Down @@