master branch

conf/hgi.config

@@ -0,0 +1,76 @@
+process {
+    cache = 'lenient'
+    shell = ['/bin/bash', '-euo', 'pipefail']
+
+    errorStrategy = { task.attempt <= 3 ? 'retry' : 'finish' }
+    maxRetries    = 3
+
+    withName: 'GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK' {
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'GATK4_GENOMICSDBIMPORT' {
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+        clusterOptions  = { "-R \"rusage[tmp=20G]\"" }
+        ext.args        = "--batch-size 50 --reader-threads 1 -ip 500"
+    }
+
+    withName: 'GATK4_GENOTYPEGVCFS' {
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+        clusterOptions  = { "-R \"rusage[tmp=20G]\"" }
+        ext.args        = { "-G StandardAnnotation -G AS_StandardAnnotation" }
+    }
+
+    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS'{
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+    }
+
+    withName:'GATK4_MERGEVCFS'{
+        cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'GATK4_HAPLOTYPECALLER' {
+    	cpus            = { check_max( 1 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 8.GB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'MERGE_HAPLOTYPECALLER' {
+		memory          = { check_max( 2.GB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' {
+        memory          = { check_max( 256.MB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'BCFTOOLS_STATS' {
+        memory          = { check_max( 128.MB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'VCFTOOLS_TSTV_COUNT|VCFTOOLS_TSTV_QUAL|VCFTOOLS_SUMMARY' {
+        memory          = { check_max( 128.MB * task.attempt, 'memory' ) }
+    }
+
+    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
+        memory          = { check_max( 128.MB * task.attempt, 'memory' ) }
+    }
+
+    withName: 'MULTIQC' {
+        cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
+        memory          = { check_max( 2.GB * task.attempt, 'memory' ) }
+    }
+}
+
+singularity {
+	autoMounts   = true
+    enabled      = true
+    cacheDir     = '/nfs/hgi/singularityContainers/'
+}
+
+executor {
+    queueSize    = 4000
+}

conf/modules/haplotypecaller.config

@@ -16,9 +16,9 @@
 process {
 
     withName: 'GATK4_HAPLOTYPECALLER' {
-        ext.args         = { params.joint_germline ? "-ERC GVCF" : "" }
+        ext.args         = { params.joint_germline ? "-ERC GVCF -G StandardAnnotation -G AS_StandardAnnotation -G StandardHCAnnotation" : "" }
         ext.prefix       = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) }
-        ext.when         = { params.tools && params.tools.split(',').contains('haplotypecaller') }
+        ext.when         = { params.tools && params.tools.split(',').any{ it.startsWith('haplotypecaller') } }
         publishDir       = [
             mode: params.publish_dir_mode,
             path: { "${params.outdir}/variant_calling/"},

conf/modules/joint_germline.config

@@ -51,15 +51,15 @@ process {
 
     withName: 'VARIANTRECALIBRATOR_INDEL' {
         ext.prefix = { "${meta.id}_INDEL" }
-        ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP  -mode INDEL"
+        ext.args = "-AS -an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP  -mode INDEL"
         publishDir = [
             enabled: false
         ]
     }
 
     withName: 'VARIANTRECALIBRATOR_SNP' {
         ext.prefix = { "${meta.id}_SNP" }
-        ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
+        ext.args = "-AS -an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP"
         publishDir = [
             enabled: false
         ]

modules/local/create_intervals_bed/main.nf

@@ -28,11 +28,12 @@ process CREATE_INTERVALS_BED {
                 # no runtime estimate in this row, assume default value
                 t = (\$3 - \$2) / ${params.nucleotides_per_second}
             }
-            if (name == "" || (chunk > 600 && (chunk + t) > longest * 1.05)) {
+            if (name == "" || (chunk > 600 && (chunk + t) > longest * 1.00) || \$1 != chr) {
                 # start a new chunk
                 name = sprintf("%s_%d-%d.bed", \$1, \$2+1, \$3)
                 chunk = 0
                 longest = 0
+                chr = \$1
             }
             if (t > longest)
                 longest = t

nextflow.config

@@ -242,6 +242,8 @@ profiles {
         executor.memory        = 8.GB
         executor.name          = 'local'
     }
+    // Custom profile
+    hgi                        { includeConfig 'conf/hgi.config' }
     // Basic test profile for CI
     test                       { includeConfig 'conf/test.config' }
     test_cache                 { includeConfig 'conf/test/cache.config' }