diff --git a/conf/pipeline/eager/eva.config b/conf/pipeline/eager/eva.config index f35f1ed..f633bae 100644 --- a/conf/pipeline/eager/eva.config +++ b/conf/pipeline/eager/eva.config @@ -9,7 +9,7 @@ params { // Specific nf-core/eager process configuration process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -69,17 +69,17 @@ process { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc_after_clipping { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } - errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } + errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } withName: adapter_removal { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: bwa { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga())}G,h=!(bionode01|bionode02|bionode03|bionode04|bionode05|bionode06)" } } @@ -188,19 +188,19 @@ process { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName:get_software_versions { cache = false clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName:eigenstrat_snp_coverage { beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' - } - + } + withName:kraken_merge { beforeScript = 'export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' } @@ -226,7 +226,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -279,7 +279,7 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc_after_clipping { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } @@ -404,7 +404,7 @@ profiles { process { - beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' + beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"' maxRetries = 2 @@ -457,7 +457,7 @@ profiles { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } } - + withName: fastqc_after_clipping { clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G" } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }