Merge pull request #23 from CCBR/dev/feature-SVCNV

Dev/feature svcnv
CCBR · Dec 6, 2023 · 07aa992 · 07aa992
2 parents a55b5d4 + f06b472
commit 07aa992
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Showing 3 changed files with 14 additions and 6 deletions.
diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile
@@ -45,6 +45,14 @@ RUN wget https://github.com/biod/sambamba/releases/download/v0.8.1/sambamba-0.8.
     && mv /opt2/sambamba-0.8.1-linux-amd64-static /opt2/sambamba \
     && chmod a+rx /opt2/sambamba
 
+# Install GATK4 (GATK/4.4.0.0)
+# Requires Java17 
+RUN wget https://github.com/broadinstitute/gatk/releases/download/4.4.0.0/gatk-4.4.0.0.zip \
+    && unzip /opt2/gatk-4.4.0.0.zip \
+    && rm /opt2/gatk-4.4.0.0.zip \
+    && /opt2/gatk-4.4.0.0/gatk --list
+ENV PATH="/opt2/gatk-4.4.0.0:$PATH"
+
 # Use DISCVRSeq For CombineVariants Replacement
 RUN wget https://github.com/BimberLab/DISCVRSeq/releases/download/1.3.62/DISCVRSeq-1.3.62.jar 
 ENV DISCVRSeq_JAR="/opt2/DISCVRSeq-1.3.62.jar"

diff --git a/nextflow.config b/nextflow.config
@@ -120,7 +120,7 @@ profiles {
                 autoMounts = true
                 cacheDir = "$PWD/singularity"
                 envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
-                runOptions = '-B /gs10,/gs11,/gs12,/gs8,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
+                runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
             }    
     }
 
@@ -276,7 +276,7 @@ profiles {
                 autoMounts = true
                 cacheDir = "$PWD/singularity"
                 envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOBID'
-                runOptions = '-B /gs10,/gs11,/gs12,/gs8,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
+                runOptions = '-B /gs10,/gs11,/gs12,/gs9,/spin1,/data/CCBR_Pipeliner/,/data/CCBR_Pipeliner/Pipelines/XAVIER/resources/,/data/nousomedr/,/data/CCBR/projects/,/vf/users,/gpfs,/fdb'
             }
     }
 

diff --git a/workflow/modules/workflows_tonly.nf b/workflow/modules/workflows_tonly.nf
@@ -202,7 +202,7 @@ workflow VC_TONLY {
 
 
     emit:
-        somaticcall_input=combineVariants_octopus.out
+        somaticcall_input=octopus_in_tonly
 
 
 }
@@ -320,10 +320,10 @@ workflow INPUT_TONLY_BAM {
     main:
     //Either BAM Input or File sheet input 
     if(params.bam_input){
-        bambai=params.bam_input +".bai"
+        bambai = params.bam_input +".bai"
         baionly = bambai.replace(".bam", "")
-        bamcheck1=file(bambai)
-        bamcheck2=file(baionly)
+        bamcheck1 = file(bambai)
+        bamcheck2 = file(baionly)
 
         if (bamcheck1.size()>0){
             baminputonly=Channel.fromPath(params.bam_input)