Resource requirement tweaks

modules/local/amber/main.nf

@@ -23,14 +23,16 @@ process AMBER {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
     def reference_bam_arg = normal_bam ? "-reference_bam ${normal_bam}" : ''
 
     def target_regions_bed_arg = target_region_bed ? "-target_regions_bed ${target_region_bed}" : ''
 
     """
     amber \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -tumor ${meta.tumor_id} \\
         -tumor_bam ${tumor_bam} \\

modules/local/bamtools/main.nf

@@ -22,9 +22,11 @@ process BAMTOOLS {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     bamtools \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         com.hartwig.hmftools.bamtools.metrics.BamMetrics \\
         ${args} \\
         -sample ${meta.sample_id} \\

modules/local/cobalt/main.nf

@@ -23,6 +23,8 @@ process COBALT {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
     def reference_bam_arg = normal_bam ? "-reference_bam ${normal_bam}" : ''
 
@@ -31,7 +33,7 @@ process COBALT {
 
     """
     cobalt \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -tumor ${meta.tumor_id} \\
         -tumor_bam ${tumor_bam} \\

modules/local/cuppa/main.nf

@@ -23,6 +23,8 @@ process CUPPA {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     # Symlink input files into a single directory
     mkdir -p sample_data/
@@ -45,7 +47,7 @@ process CUPPA {
     mkdir -p cuppa/
 
     cuppa \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -sample_data_dir sample_data/ \\

modules/local/gripss/germline/main.nf

@@ -28,9 +28,11 @@ process GRIPSS_GERMLINE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     gripss \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.normal_id} \\
         -reference ${meta.tumor_id} \\

modules/local/gripss/somatic/main.nf

@@ -29,13 +29,15 @@ process GRIPSS_SOMATIC {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
     def target_regions_bed_arg = target_region_bed ? "-target_regions_bed ${target_region_bed}" : ''
     def output_id_arg = meta.containsKey('normal_id') ? '-output_id somatic' : ''
 
     """
     gripss \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.tumor_id} \\
         ${reference_arg} \\

modules/local/isofox/main.nf

@@ -30,6 +30,8 @@ process ISOFOX {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def functions_arg = functions ? "-functions \'${functions}\'" : ''
 
     def exp_counts_arg = exp_counts ? "-exp_counts_file ${exp_counts}" : ''
@@ -42,7 +44,7 @@ process ISOFOX {
     mkdir -p isofox/
 
     isofox \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -bam_file ${bam} \\

modules/local/lilac/main.nf

@@ -23,6 +23,8 @@ process LILAC {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def sample_name = getSampleName(meta, tumor_dna_bam, normal_dna_bam)
 
     def normal_bam_arg = normal_dna_bam ? "-reference_bam ${normal_dna_bam}" : ''
@@ -33,7 +35,7 @@ process LILAC {
 
     """
     lilac \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${sample_name} \\
         ${normal_bam_arg} \\

modules/local/linx/germline/main.nf

@@ -23,9 +23,11 @@ process LINX_GERMLINE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -sv_vcf ${sv_vcf} \\

modules/local/linx/somatic/main.nf

@@ -24,9 +24,11 @@ process LINX_SOMATIC {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -sv_vcf ${purple_dir}/${meta.sample_id}.purple.sv.vcf.gz \\

modules/local/linx/visualiser/main.nf

@@ -23,6 +23,8 @@ process LINX_VISUALISER {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     # NOTE(SW): the output plot directories are always required for ORANGE, which is straightfoward to handle with POSIX
     # fs but more involved with FusionFS since it will not write empty directories to S3. A placeholder file can't be
@@ -43,7 +45,7 @@ process LINX_VISUALISER {
     # Generate all chromosome and cluster plots by default
 
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         com.hartwig.hmftools.linx.visualiser.SvVisualiser \\
         ${args} \\
         -sample ${meta.sample_id} \\
@@ -66,7 +68,7 @@ process LINX_VISUALISER {
     # https://github.com/hartwigmedical/hmftools/blob/linx-v1.24.1/linx/src/main/java/com/hartwig/hmftools/linx/visualiser/SampleData.java#L220-L236
 
     linx \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         com.hartwig.hmftools.linx.visualiser.SvVisualiser \\
         ${args2} \\
         -sample ${meta.sample_id} \\

modules/local/markdups/main.nf

@@ -27,11 +27,13 @@ process MARKDUPS {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     def umi_flags = has_umis ? '-umi_enabled -umi_duplex -umi_duplex_delim +' : ''
 
     """
     markdups \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         \\
         -samtools \$(which samtools) \\

modules/local/orange/main.nf

@@ -31,6 +31,8 @@ process ORANGE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     def pipeline_version_str = pipeline_version ?: 'not specified'
 
     def virus_dir_arg = virusinterpreter_dir ? "-virus_dir ${virusinterpreter_dir}" : ''
@@ -104,7 +106,7 @@ process ORANGE {
 
     java \\
         --add-opens java.base/java.time=ALL-UNNAMED \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         -jar \${orange_jar} \\
             ${args} \\
             \\

modules/local/pave/germline/main.nf

@@ -35,6 +35,8 @@ process PAVE_GERMLINE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def gnomad_args
     if (genome_ver.toString() == '37') {
         gnomad_args = "-gnomad_freq_file ${gnomad_resource}"
@@ -46,7 +48,7 @@ process PAVE_GERMLINE {
 
     """
     pave \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -vcf_file ${sage_vcf} \\

modules/local/pave/somatic/main.nf

@@ -31,6 +31,8 @@ process PAVE_SOMATIC {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def pon_filters
     def gnomad_args
     if (genome_ver.toString() == '37') {
@@ -48,7 +50,7 @@ process PAVE_SOMATIC {
 
     """
     pave \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -vcf_file ${sage_vcf} \\

modules/local/purple/main.nf

@@ -1,6 +1,6 @@
 process PURPLE {
     tag "${meta.id}"
-    label 'process_low'
+    label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -33,6 +33,8 @@ process PURPLE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
 
     def sv_tumor_vcf_arg = sv_tumor_vcf ? "-somatic_sv_vcf ${sv_tumor_vcf}" : ''
@@ -52,7 +54,7 @@ process PURPLE {
 
     """
     purple \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -tumor ${meta.tumor_id} \\
         ${reference_arg} \\

modules/local/sage/append/main.nf

@@ -24,9 +24,11 @@ process SAGE_APPEND {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     sage \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         com.hartwig.hmftools.sage.append.SageAppendApplication \\
         ${args} \\
         -input_vcf ${vcf} \\

modules/local/sage/germline/main.nf

@@ -1,6 +1,6 @@
 process SAGE_GERMLINE {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -30,11 +30,13 @@ process SAGE_GERMLINE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     """
     mkdir germline/
 
     sage \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -tumor ${meta.normal_id} \\
         -tumor_bam ${normal_bam} \\

modules/local/sage/somatic/main.nf

@@ -2,7 +2,7 @@
 
 process SAGE_SOMATIC {
     tag "${meta.id}"
-    label 'process_medium'
+    label 'process_high'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -32,14 +32,16 @@ process SAGE_SOMATIC {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     def reference_arg = meta.containsKey('normal_id') ? "-reference ${meta.normal_id}" : ''
     def reference_bam_arg = normal_bam ? "-reference_bam ${normal_bam}" : ''
 
     """
     mkdir -p somatic/
 
     sage \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         ${reference_arg} \\
         ${reference_bam_arg} \\

modules/local/sigs/main.nf

@@ -21,11 +21,13 @@ process SIGS {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     """
     mkdir -p sigs/
 
     sigs \\
-        -Xmx${Math.round(task.memory.bytes * 0.95)} \\
+        -Xmx${Math.round(task.memory.bytes * xmx_mod)} \\
         ${args} \\
         -sample ${meta.sample_id} \\
         -somatic_vcf_file ${smlv_vcf} \\

modules/local/svprep/assemble/main.nf

@@ -26,6 +26,8 @@ process GRIDSS_ASSEMBLE {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.95
+
     def config_arg = gridss_config ? "--configuration ${gridss_config}" : ''
     def output_dirname = 'gridss_assemble'
     def labels_list = labels instanceof List ? labels : [labels]
@@ -74,7 +76,7 @@ process GRIDSS_ASSEMBLE {
     # Run
     gridss_svprep \\
         ${args} \\
-        --jvmheap ${Math.round((task.memory.bytes - otherJvmHeap) * 0.95)} \\
+        --jvmheap ${Math.round((task.memory.bytes - otherJvmHeap) * xmx_mod)} \\
         --otherjvmheap ${otherJvmHeap} \\
         --steps assemble \\
         --labels ${labels_arg} \\

modules/local/svprep/call/main.nf

@@ -26,6 +26,8 @@ process GRIDSS_CALL {
     script:
     def args = task.ext.args ?: ''
 
+    def xmx_mod = task.ext.xmx_mod ?: 0.75
+
     def config_arg = gridss_config ? "--configuration ${gridss_config}" : ''
     def output_dirname = 'gridss_call'
     def labels_list = labels instanceof List ? labels : [labels]
@@ -72,7 +74,7 @@ process GRIDSS_CALL {
     # Run
     gridss_svprep \\
         ${args} \\
-        --jvmheap ${Math.round((task.memory.bytes - otherJvmHeap) * 0.95)} \\
+        --jvmheap ${Math.round((task.memory.bytes - otherJvmHeap) * xmx_mod)} \\
         --otherjvmheap ${otherJvmHeap} \\
         --steps call \\
         --labels ${labels_arg} \\