Dev fix resource tags

conf/base.config

@@ -32,27 +32,69 @@ process {
         maxRetries    = 2
     }
 
+    // === CPU TIERS ===
+    // Label-based, cpus only. Memory/time stay in the withName overrides
+    // below so per-process tuning isn't blocked by a shared label. No
+    // label for cpus=1: that's already the global default above.
+    withLabel: cpu_low {
+        cpus = { 2 * task.attempt }
+    }
+    withLabel: cpu_medium {
+        cpus = { 4 * task.attempt }
+    }
+    withLabel: cpu_high {
+        cpus = { 8 * task.attempt }
+    }
+
+    // === MEMORY TIERS ===
+    // Only one label: processes verified (via peak_rss trace data) to stay
+    // under 1 GB, where the 4 GB global default is wasteful at scale.
+    // Anything above 4 GB gets a dedicated withName override instead
+    // (see e.g. DNDS:PREPROCESSDEPTHS, MUTABILITY.*:RELATIVEMUTABILITY
+    // below) so tuning stays per-process rather than a shared label.
+    withLabel: mem_low {
+        memory = { 1.GB * task.attempt }
+    }
+
     // === PANEL CREATION PROCESSES ===
     // Large memory requirements for genomic position processing
     withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:SITESFROMPOSITIONS' {
         memory = { 8.GB * task.attempt }
     }
 
-    // VEP annotation is CPU and memory intensive for large VCFs
+    // VEP annotation is CPU and memory intensive for large VCFs.
+    // Exception to the cpu-tier labels: verified via real trace data at
+    // ~1200-1400% cpu (12-14 cores used out of 24 requested) on panel chunks.
     withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:VCFANNOTATEPANEL:ENSEMBLVEP_VEP*' {
         cpus   = { 24 * task.attempt }
         memory = { 6.GB * task.attempt }
     }
 
+    // Per-sample VEP annotation: no label (module is nf-core, unlabeled);
+    // kept as its own cpus override, same as the panel one above.
+    withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:VCFANNOTATE:ENSEMBLVEP_VEP*' {
+        cpus = { 24 * task.attempt }
+    }
+
     withName: 'CUSTOMPROCESSING.*' {
         memory = { 10.GB * task.attempt }
     }
 
+    // Exception to the cpu-tier labels: TABIX_BGZIPTABIX_QUERY is a shared
+    // nf-core module reused under many other aliases (QUERYMUTATIONS,
+    // QUERYDEPTHS, QUERYPANEL...) that don't need extra cpus, so this can't
+    // be a module-level label without affecting those too.
     withName: 'BBGTOOLS:DEEPCSA:DEPTHS.*CONS' {
         cpus   = { 2 * task.attempt }
         memory = { 8.GB * task.attempt }
     }
 
+    // Same shared module, different aliases: these query mutation tables
+    // (not depths), peak_rss well under 1 GB.
+    withName: 'QUERYMUTATIONS|QUERYMUTATIONSEXONS' {
+        memory = { 1.GB * task.attempt }
+    }
+
     withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATECAPTUREDPANELS*' {
         memory = { 6.GB * task.attempt }
     }
@@ -68,7 +110,6 @@ process {
     }
 
     withName: '(BBGTOOLS:DEEPCSA:CREATEPANELS:DOMAINANNOTATION*)' {
-        cpus   = { 2 * task.attempt }
         memory = { 10.GB * task.attempt }
     }
 
@@ -84,36 +125,77 @@ process {
         memory = { 12.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:SOMATICMUTATIONS*' {
-        cpus   = { 1 * task.attempt }
-        memory = { 1.GB * task.attempt }
-    }
-
     withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:POSTPROCESSVEPPANEL*' {
-        cpus   = { 2 * task.attempt }
         memory = { 8.GB * task.attempt }
     }
 
-    // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING
-    withName: 'PREPROCESSING|ESTIMATOR' {
+    // BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING(GLOBALLOC): peak_rss ~2.6 GB, well under
+    // the 4 GB default.
+    withName: 'PREPROCESSING' {
         memory = { 4.GB * task.attempt }
     }
 
+    // BBGTOOLS:DEEPCSA:{OMEGA,OMEGAMULTI}:{ESTIMATOR,ESTIMATORGLOBALLOC}: peak_rss up
+    // to ~24.3 GB on the largest gene sets. The old 4 GB tier maxed out at 16 GB after
+    // 3 retries, so the biggest tasks could never succeed. +20% headroom.
+    withName: 'ESTIMATOR|ESTIMATORGLOBALLOC' {
+        memory = { 30.GB * task.attempt }
+    }
+
     // BBGTOOLS:DEEPCSA:SIGNATURESNONPROT:SIGPROFILERASSIGNMENT
     withName: 'SIGPROFILERASSIGNMENT' {
         memory = { 2.GB * task.attempt }
     }
 
+    // peak_rss 33-33.4 GB (BDO_duplexome / all_samples) -> +20% headroom
+    withName: 'BBGTOOLS:DEEPCSA:DNDS:PREPROCESSDEPTHS' {
+        memory = { 40.GB * task.attempt }
+    }
+
+    // peak_rss 36.1-36.9 GB, same order of magnitude on both MUTABILITYALL
+    // and MUTABILITYNONPROT (BDO_duplexome / all_samples) -> +19% headroom
+    withName: 'BBGTOOLS:DEEPCSA:MUTABILITY.*:RELATIVEMUTABILITY' {
+        memory = { 44.GB * task.attempt }
+    }
+
+    // peak_rss up to 39.4 GB on the largest cohorts; no override existed before, so it
+    // defaulted to 4 GB and could never succeed (63% FAILED in resources_test run). +20% headroom.
+    withName: 'BBGTOOLS:DEEPCSA:ONCODRIVE3D:ONCODRIVE3D_RUN' {
+        memory = { 48.GB * task.attempt }
+    }
+
+    // peak_rss up to 12 GB; no override existed, so every sample needed ~2 retries
+    // against the 4 GB default before landing on enough memory. +25% headroom so it
+    // succeeds on the first attempt.
+    withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:FILTERNANOSEQNOISE' {
+        memory = { 15.GB * task.attempt }
+    }
+
+    // peak_rss up to 6.3 GB; the 4 GB default meant every one of the 128 samples
+    // failed on the first attempt and only succeeded on the 8 GB retry. Setting the
+    // base to 8 GB avoids that guaranteed-fail-then-retry pattern.
+    withName: 'BBGTOOLS:DEEPCSA:MUTDENSITYALL:MUTDENSITY' {
+        memory = { 8.GB * task.attempt }
+    }
+
+    // Same process handles per-sample and per-cohort ("all_samples", "Ismale0/1",
+    // "Samplelocation*") runs -- can't select by tag, only by process name. The
+    // cohort runs were getting OOM-killed by Slurm (71-113 oom_kill events per job)
+    // under the 4 GB default; individual samples fit comfortably under 3 GB. No clean
+    // peak_rss from the killed runs to calibrate against, so 24 GB is an estimate --
+    // revisit once a run confirms the real peak. cpus fixed (not cpu_high's
+    // 8*attempt) so retries actually gain memory headroom per core instead of just
+    // scaling both in lockstep.
+    withName: 'BBGTOOLS:DEEPCSA:ONCODRIVEFMLALL:ONCODRIVEFMLSNVS' {
+        cpus   = { 8 }
+        memory = { 24.GB * task.attempt }
+    }
+
     // === UTILITY PROCESSES ===
     withName: 'BBGTOOLS:DEEPCSA:CUSTOM_DUMPSOFTWAREVERSIONS*' {
         cache = false
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:DEPTHANALYSIS:COMPUTEDEPTHS' {
-        cpus = { 4 * task.attempt }
-        memory = { 4.GB * task.attempt }
-    }
-
     withName: 'MUTATEDGENOMESFROMVAFAM' {
         errorStrategy = 'ignore'
         maxRetries = 1
@@ -124,12 +206,18 @@ process {
         maxRetries = 1
     }
 
+    withName: 'BBGTOOLS:DEEPCSA:PLOTTINGSUMMARY:PLOTSATURATION' {
+        errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
+        maxRetries = 4
+    }
+
     withName: 'BBGTOOLS:DEEPCSA:PLOTTINGQC:PLOTMUTATIONSPECIFIC' {
         memory = { 24.GB * task.attempt }
     }
 
     withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:DNA2PROTEINMAPPING' {
         memory = { 30.GB * task.attempt }
+        errorStrategy = 'ignore'
     }
 
     withName: 'FILTERNANOSEQSNP' {

conf/deepcsa_config_bbgregressions_test.config

@@ -100,14 +100,17 @@ params {
 }
 
 process {
-    withLabel: process_high_memory {
+    withLabel: cpu_high {
         cpus   = { 2 * task.attempt }
-        memory = { 15.GB * task.attempt }
+        memory = { 16.GB * task.attempt }
     }
 
-    withLabel: process_high {
-        cpus   = { 2 * task.attempt }
-        memory = { 16.GB * task.attempt }
-        time   = { 1.h * task.attempt }
+    // base.config sizes these for real cohorts (40/44 GB); cap them back
+    // down for the minimal test dataset.
+    withName: 'BBGTOOLS:DEEPCSA:DNDS:PREPROCESSDEPTHS' {
+        memory = { 15.GB * task.attempt }
+    }
+    withName: 'BBGTOOLS:DEEPCSA:MUTABILITY.*:RELATIVEMUTABILITY' {
+        memory = { 15.GB * task.attempt }
     }
 }

conf/mice.config

@@ -77,8 +77,3 @@ params {
 }
 
 
-process {
-    withLabel: process_high_memory {
-        memory = { 15.GB * task.attempt }
-    }
-}

conf/test_real.config

@@ -97,14 +97,17 @@ params {
 }
 
 process {
-    withLabel: process_high_memory {
+    withLabel: cpu_high {
         cpus   = { 2 * task.attempt }
-        memory = { 15.GB * task.attempt }
+        memory = { 16.GB * task.attempt }
     }
 
-    withLabel: process_high {
-        cpus   = { 2 * task.attempt }
-        memory = { 16.GB * task.attempt }
-        time   = { 1.h * task.attempt }
+    // base.config sizes these for real cohorts (40/44 GB); cap them back
+    // down for the minimal test dataset.
+    withName: 'BBGTOOLS:DEEPCSA:DNDS:PREPROCESSDEPTHS' {
+        memory = { 15.GB * task.attempt }
+    }
+    withName: 'BBGTOOLS:DEEPCSA:MUTABILITY.*:RELATIVEMUTABILITY' {
+        memory = { 15.GB * task.attempt }
     }
 }

modules/local/analyzedepths/main.nf

@@ -1,6 +1,6 @@
 process ANALYZE_DEPTHS_GROUPS {
     tag "groups"
-    label 'process_low'
+    label 'cpu_low'
 
     label 'deepcsa_core'
 

modules/local/bbgtools/bbgregressions/create_input/main.nf

@@ -1,7 +1,6 @@
 process CREATE_INPUT {
 
     tag "regressions"
-    label 'process_single'
 
     label "bbgregressions"
 

modules/local/bbgtools/bbgregressions/editconfig/main.nf

@@ -1,7 +1,7 @@
 process EDITCONFIG {
 
     tag "regressions"
-    label 'process_low'
+    label 'cpu_low'
 
     label "bbgregressions"
 

modules/local/bbgtools/bbgregressions/plot/main.nf

@@ -1,7 +1,6 @@
 process PLOT {
 
     tag "regressions"
-    label 'process_single'
 
     label "bbgregressions"
 

modules/local/bbgtools/bbgregressions/regressions/main.nf

@@ -1,7 +1,6 @@
 process REGRESSIONS {
 
     tag "regressions"
-    label 'process_single'
 
     label "bbgregressions"
 

modules/local/bbgtools/omega/estimator/main.nf

@@ -1,8 +1,6 @@
 process OMEGA_ESTIMATOR {
     tag "$meta.id"
     label 'cpu_medium'
-    label 'time_low'
-    label 'process_high_memory'
 
 
     container 'docker.io/bbglab/omega:0.2.1'

modules/local/bbgtools/omega/mutabilities/main.nf

@@ -1,8 +1,5 @@
 process OMEGA_MUTABILITIES {
     tag "$meta.id"
-    label 'cpu_single_fixed'
-    label 'time_low'
-    label 'process_high_memory'
 
 
     container 'docker.io/bbglab/omega:0.2.1'

modules/local/bbgtools/oncodrive3d/plot/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVE3D_PLOT {
     tag "$meta.id"
-    label 'process_medium'
+    label 'cpu_medium'
 
     container 'docker.io/spellegrini87/oncodrive3d:1.0.9-light'
 

modules/local/bbgtools/oncodrive3d/plot_chimerax/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVE3D_PLOT_CHIMERAX {
     tag "$meta.id"
-    label 'process_medium'
+    label 'cpu_medium'
 
     container 'docker.io/spellegrini87/oncodrive3d:1.0.9-chimerax'
 

modules/local/bbgtools/oncodrive3d/preprocessing/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVE3D_PREPROCESSING {
     tag "$meta.id"
-    label 'process_medium'
+    label 'cpu_medium'
 
     label 'deepcsa_core'
 

modules/local/bbgtools/oncodrive3d/run/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVE3D_RUN {
     tag "$meta.id"
-    label 'process_high'
+    label 'cpu_high'
 
     container 'docker.io/spellegrini87/oncodrive3d:1.0.9-light'
 

modules/local/bbgtools/oncodriveclustl/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVECLUSTL {
     tag "$meta.id"
-    label 'process_high'
+    label 'cpu_high'
 
     // // conda "YOUR-TOOL-HERE"
     // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/bbgtools/oncodrivefml/main.nf

@@ -1,6 +1,6 @@
 process ONCODRIVEFML {
     tag "$meta.id"
-    label 'process_high'
+    label 'cpu_high'
 
     container 'docker.io/ferriolcalvet/oncodrivefml:latest'
 

modules/local/bbgtools/sitecomparison/main.nf

@@ -1,8 +1,5 @@
 process SITE_COMPARISON {
     tag "$meta.id"
-    label 'cpu_single_fixed'
-    label 'time_low'
-    label 'process_high_memory'
 
     label 'deepcsa_core'
 

modules/local/blacklistmuts/main.nf

@@ -1,7 +1,7 @@
 process BLACKLIST_MUTATIONS {
 
     tag "$meta.id"
-    label 'process_low'
+    label 'cpu_low'
 
     label 'deepcsa_core'
 

modules/local/compute_mutability/main.nf

@@ -1,8 +1,7 @@
 process COMPUTE_RELATIVE_MUTABILITY {
 
     tag "$meta.id"
-    label 'process_low_fixed_cpus'
-    label 'process_high_memory'
+    label 'cpu_low'
 
     label 'deepcsa_core'
 

modules/local/compute_profile/main.nf

@@ -1,7 +1,8 @@
 process COMPUTE_PROFILE {
 
     tag "$meta.id"
-    label 'process_low'
+    label 'cpu_low'
+    label 'mem_low'
 
 
     label 'deepcsa_core'

modules/local/compute_trinucleotide/main.nf

@@ -1,7 +1,7 @@
 process COMPUTE_TRINUCLEOTIDE {
 
     tag "$meta.id"
-    label 'process_low'
+    label 'cpu_low'
 
     label 'deepcsa_core'