Merge pull request #19 from CCBR/dev/feature-SVCNV

Update docker java version
CCBR · Nov 22, 2023 · 21d7526 · 21d7526
2 parents 095b8ed + 065aea9
commit 21d7526
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Showing 11 changed files with 325 additions and 348 deletions.
diff --git a/conf/hg38.config b/conf/hg38.config
@@ -1,9 +1,10 @@
 params {
     genomes {
         'hg38' {
-            genome = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta" // file(params.genome) 
+            genome = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta" 
+            genomefai = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/bwamem2/Homo_sapiens_assembly38.fasta.fai" 
             genomedict= "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/genome/Homo_sapiens_assembly38.dict"
-            wgsregion = "/data/nousomedr/annotation/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list" //
+            wgsregion = "/data/nousomedr/annotation/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list" 
             intervals="${projectDir}/workflow/resources/hg38_v0_wgs_calling_regions.hg38.bed"
             //millsindel = "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" //Mills_and_1000G_gold_standard.indels.hg38.vcf.gz"
             //shapeitindel =  "/data/CCBR_Pipeliner/CCBR_Pipeliner_Legacy/Exome-seek/hg38/GATK_resource_bundle/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz" //file(params.gold_indels2) //

diff --git a/conf/mm10.config b/conf/mm10.config
@@ -2,6 +2,7 @@ params {
     genomes {
         'mm10' {
             genome = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa" // file(params.genome) 
+            genomefai = "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.fa.fai" // file(params.genome) 
             bwagenome= "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwaindex/genome.fa"
             genomedict= "/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/mm10/genome/bwamem2index/genome.dict"
             //FIXwgsregion = "/data/nousomedr/annotation/resources_broad_hg38_v0_wgs_calling_regions.hg38.interval_list" //

diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile
@@ -17,10 +17,12 @@ WORKDIR /opt2
 # This section installs system packages required for your project
 # If you need extra system packages add them here.
 # python/3.8.0 and python/2.7.16 (strelka and manta)
+# JDK 17 for DISCVRSeq
 RUN apt-get update \
  && apt-get -y upgrade \
  && DEBIAN_FRONTEND=noninteractive apt-get install -y \
-      bc    
+      bc \
+      openjdk-17-jdk   
 
 # Common bioinformatics tools 
 # bwa/0.7.17-4  bowtie/1.2.3  bowtie2/2.3.5.1 
@@ -158,15 +160,6 @@ RUN wget https://github.com/AstraZeneca-NGS/VarDictJava/releases/download/v1.8.3
     && rm /opt2/VarDict-1.8.3.tar
 ENV PATH="/opt2/VarDict-1.8.3/bin:$PATH"
 
-# Install Octopus/v0.7.4
-#RUN wget https://github.com/luntergroup/octopus/archive/refs/tags/v0.7.4.tar.gz \ 
-#    && tar -xvzf /opt2/v0.7.4.tar.gz \
-#    && rm /opt2/v0.7.4.tar.gz \
-#    && cd /opt2/octopus-0.7.4 \
-#    && cmake .
-#ENV PATH="/opt2/octopus-0.7.4/bin:$PATH"
-
-
 # Fastp From Opengene github
 RUN wget http://opengene.org/fastp/fastp.0.23.2 \
     && mkdir fastp \

diff --git a/docker/logan_base/build.sh b/docker/logan_base/build.sh
@@ -5,8 +5,10 @@
 #docker buildx build --platform linux/amd64 -f Dockerfile -t dnousome/ccbr_logan_base:v0.3.0 -t dnousome/ccbr_logan_base:latest --push .
 
 docker build --platform linux/amd64 --tag ccbr_logan_base:v0.3.3 -f Dockerfile . 
-docker tag ccbr_logan_base:v0.3.0 dnousome/ccbr_logan_base:v0.3.3
-docker tag ccbr_logan_base:v0.3.0 dnousome/ccbr_logan_base
+
+docker tag ccbr_logan_base:v0.3.3 dnousome/ccbr_logan_base:v0.3.3
+docker tag ccbr_logan_base:v0.3.3 dnousome/ccbr_logan_base
+
 
 docker push dnousome/ccbr_logan_base:v0.3.3
 docker push dnousome/ccbr_logan_base:latest

diff --git a/nextflow.config b/nextflow.config
@@ -23,6 +23,7 @@ params {
     script_freecpaired = "${projectDir}/workflow/scripts/freec_paired.pl"
     freec_significance = "${projectDir}/workflow/scripts/assess_significance.R"
     freec_plot = "${projectDir}/workflow/scripts/makeGraph.R"
+    lofreq_convert = "${projectDir}/workflow/scripts/lofreq_convert.sh"
     vep_cache = "/fdb/VEP/102/cache"
 
     //Biowulf
@@ -69,19 +70,19 @@ profiles {
         process {
             executor = 'local'
             withLabel: process_low {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1' 
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3' 
             }
             withLabel: process_mid {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1' 
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3' 
             }
             withLabel: process_highcpu {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1' 
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3' 
             }
             withLabel: process_highmem {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1' 
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3' 
             }
             withLabel: process_somaticcaller {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1' 
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3' 
             }
             withName:fastq_screen {
                 container = 'docker://nciccbr/ccbr_fastq_screen_0.13.0:v2.0' 
@@ -191,7 +192,7 @@ profiles {
                 }
             //Other Processes
             withName:bwamem2 {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory=150.GB
                 time=48.h
                 cpus=16
@@ -235,30 +236,30 @@ profiles {
             }
             //Global Processes
             withLabel: process_low {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory = 16.GB
                 time = 12.h
                 cpus = 2
             }
             withLabel: process_mid {               
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory=24.GB
                 time=24.h
                 cpus=4
             }
             withLabel: process_highcpu {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory = 54.GB
                 time = 72.h
                 cpus = 16
             }
             withLabel: process_highmem {
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory = 48.GB
                 time = 48.h
             }
             withLabel: process_somaticcaller {   
-                container = 'docker://dnousome/ccbr_logan_base:v0.3.1'
+                container = 'docker://dnousome/ccbr_logan_base:v0.3.3'
                 memory = 48.GB
                 cpus = 4
                 time = 72.h

diff --git a/workflow/modules/copynumber.nf b/workflow/modules/copynumber.nf
@@ -21,8 +21,6 @@ ENSEMBLCACHE='/data/SCLC-BRAINMETS/cn/common/ensembl_data'
 DRIVERS='/data/SCLC-BRAINMETS/cn/common/DriverGenePanel.38.tsv'
 HOTSPOTS='/data/SCLC-BRAINMETS/cn/variants/KnownHotspots.somatic.38.vcf.gz'
 
-
-
 //DBSNP_INDEL=file(params.genomes[params.genome].KNOWNINDELS) 
 //ascatR=
 
@@ -370,15 +368,15 @@ process purple {
         tuple val(tumorname),
         path(cobaltin), 
         path(amberin),
-        path(somaticvcf)
+        path(somaticvcf),
+        path(somaticvcfindex)
 
     output:
         tuple val(tumorname), path("${tumorname}")
 
     script:
 
     """
-
     java -jar purple.jar \
     -tumor ${tumorname} \
     -amber ${amberin} \
@@ -391,7 +389,6 @@ process purple {
     -driver_gene_panel $DRIVERS \
     -somatic_hotspots $HOTSPOTS \
     -output_dir ${tumorname}
-
     """
 
     stub: