diff --git a/docker/logan_base/Dockerfile b/docker/logan_base/Dockerfile index 41d1ede..4e60d08 100644 --- 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:$PATH" + # Use DISCVRSeq For CombineVariants Replacement RUN wget https://github.com/BimberLab/DISCVRSeq/releases/download/1.3.62/DISCVRSeq-1.3.62.jar ENV DISCVRSeq_JAR="/opt2/DISCVRSeq-1.3.62.jar" diff --git a/nextflow.config b/nextflow.config index c179409..725be22 100644 --- a/nextflow.config +++ b/nextflow.config @@ -120,7 +120,7 @@ profiles { autoMounts = true cacheDir = "$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' } }