diff --git a/conf/hasta.config b/conf/hasta.config index 7e97e5a..c8c1f01 100644 --- a/conf/hasta.config +++ b/conf/hasta.config @@ -16,19 +16,29 @@ singularity { params { max_memory = 180.GB max_cpus = 36 - max_time = 336.h + max_time = 336.h } process { executor = 'slurm' - clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } + clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''}" } } profiles { - dev_prio { + stub_prio { params { priority = 'development' clusterOptions = "--qos=low" + max_memory = 6.GB + max_cpus = 1 + max_time = 1.h + } + } + + dev_prio { + params { + priority = 'development' + clusterOptions = "--qos=low" } } diff --git a/conf/pipeline/raredisease/hasta.config b/conf/pipeline/raredisease/hasta.config index c31b940..4c4d15e 100644 --- a/conf/pipeline/raredisease/hasta.config +++ b/conf/pipeline/raredisease/hasta.config @@ -1,5 +1,5 @@ process { - + withName:'PICARD_MARKDUPLICATES' { memory = { check_max( 90.GB * task.attempt, 'memory' ) } } @@ -7,6 +7,19 @@ process { cpus = { check_max( 16 * task.attempt, 'cpus' ) } memory = { check_max( 80.GB * task.attempt, 'memory' ) } } + withLabel:'sentieon' { + beforeScript = { "export PATH=\$PATH:\$SENTIEON_INSTALL_DIR/sentieon-genomics-202112.02/bin" } + } + withName: 'BCFTOOLS_VIEW' { + if (params.genome == 'GRCh37') { + ext.args = '--output-type z --apply-filters PASS --exclude "INFO/clinical_genomics_mipAF > 0.40 | INFO/swegenAF > 0.40 | INFO/clingen_ngiAF > 0.40 | INFO/gnomad_svAF > 0.40 "' + } else if (params.genome == 'GRCh38') { + ext.args = '--output-type z --apply-filters PASS --exclude "INFO/swegen_FRQ > 0.40"' + } + publishDir = [ + enabled: false, + ] + } // Java memory fixes withName:'QUALIMAP_BAMQC' { @@ -16,4 +29,4 @@ process { clusterOptions = { "-A $params.priority ${params.clusterOptions ?: ''} ${task.memory ? "--mem ${task.memory.mega * 1.15 as long}M" : ''}" } } -} \ No newline at end of file +}