diff --git a/buildContainers.nf b/buildContainers.nf index 9f96cc54b6..2c19dac666 100644 --- a/buildContainers.nf +++ b/buildContainers.nf @@ -36,7 +36,7 @@ kate: syntax groovy; space-indent on; indent-width 2; ================================================================================ */ -version = '1.2.1' +version = '1.2.2' // Check that Nextflow version is up to date enough // try / throw / catch works for NF versions < 0.25 when this was implemented diff --git a/buildReferences.nf b/buildReferences.nf index 71a636b887..950f9059c0 100644 --- a/buildReferences.nf +++ b/buildReferences.nf @@ -39,7 +39,7 @@ kate: syntax groovy; space-indent on; indent-width 2; ================================================================================ */ -version = '1.2.1' +version = '1.2.2' // Check that Nextflow version is up to date enough // try / throw / catch works for NF versions < 0.25 when this was implemented diff --git a/configuration/uppmax-localhost.config b/configuration/uppmax-localhost.config index 1fc42a9e9c..d18f507b6e 100644 --- a/configuration/uppmax-localhost.config +++ b/configuration/uppmax-localhost.config @@ -60,14 +60,14 @@ process { memory = {params.totalMemory} } $IndelRealigner { - memory = params.singleCPUMem * 2 * task.attempt + memory = {params.singleCPUMem * 2 * task.attempt} } $MapReads { cpus = 16 memory = {params.totalMemory} } $MarkDuplicates { - memory = params.singleCPUMem * 2 * task.attempt + memory = {params.singleCPUMem * 2 * task.attempt} } $MergeBams { cpus = 16 @@ -75,16 +75,16 @@ process { } $RealignerTargetCreator { cpus = 4 - memory = params.singleCPUMem * 4 * task.attempt + memory = {params.singleCPUMem * 4 * task.attempt} } $RecalibrateBam { memory = {params.singleCPUMem * task.attempt} } $RunAlleleCount { - memory = params.singleCPUMem * 2 * task.attempt + memory = {params.singleCPUMem * 2 * task.attempt} } $RunAscat { - memory = params.singleCPUMem * 2 * task.attempt + memory = {params.singleCPUMem * 2 * task.attempt} } $RunBamQC { cpus = 16 @@ -93,18 +93,18 @@ process { $RunBcftoolsStats { } $RunConvertAlleleCounts { - memory = params.singleCPUMem * 2 * task.attempt + memory = {params.singleCPUMem * 2 * task.attempt} } $RunFastQC { - errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } + errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } $RunFreeBayes { cpus = 1 - memory = { params.singleCPUMem * task.attempt} + memory = {params.singleCPUMem * task.attempt} } $RunHaplotypecaller { // Increase memory quadratically - memory = params.singleCPUMem * task.attempt * task.attempt + memory = {params.singleCPUMem * task.attempt * task.attempt} } $RunGenotypeGVCFs { } @@ -116,16 +116,16 @@ process { } $RunMutect1 { cpus = 1 - memory = { params.singleCPUMem * task.attempt} + memory = {params.singleCPUMem * task.attempt} } $RunMutect2 { cpus = 1 - memory = { params.singleCPUMem * task.attempt} + memory = {params.singleCPUMem * task.attempt} } $RunSamtoolsStats { } $RunSnpeff { - errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } + errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} memory = {params.totalMemory} // TODO Does SnpEff really require that much? } $RunStrelka { @@ -133,7 +133,7 @@ process { memory = {params.totalMemory} } $RunVEP { - errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } + errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} memory = {params.totalMemory} // TODO Does VEP really require that much? } } diff --git a/main.nf b/main.nf index 4b35746201..935a69c377 100644 --- a/main.nf +++ b/main.nf @@ -63,7 +63,7 @@ kate: syntax groovy; space-indent on; indent-width 2; ================================================================================ */ -version = '1.2.1' +version = '1.2.2' // Check that Nextflow version is up to date enough // try / throw / catch works for NF versions < 0.25 when this was implemented