chore: clean up Nextflow selector warnings and dead config

conf/base.config

@@ -44,7 +44,7 @@ process {
         memory = { 6.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CUSTOMPROCESSING.*' {
+    withName: 'CUSTOMPROCESSING.*' {
         memory = { 10.GB * task.attempt }
     }
 
@@ -89,31 +89,18 @@ process {
         memory = { 1.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROT.*:SUBSETPANEL*' {
-        cpus   = { 2 * task.attempt }
-        memory = { 4.GB * task.attempt }
-    }
-
     withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:POSTPROCESSVEPPANEL*' {
         cpus   = { 2 * task.attempt }
         memory = { 8.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:MUTRATE.*:MUTRATE*' {
-        memory = { 8.GB * task.attempt }
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:OMEGA.*:(PREPROCESSING|ESTIMATOR).*' {
-        memory = { 4.GB * task.attempt }
-    }
-
-    // Catch-all for other OMEGA estimators not explicitly configured
-    // Keep conservative settings until we have usage data
-    withName: 'BBGTOOLS:DEEPCSA:OMEGA.*:ESTIMATOR_.*' {
+    // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING
+    withName: 'PREPROCESSING|ESTIMATOR' {
         memory = { 4.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:SIGNATURESNONPROT:SIGPROFILERASSIGNMENT*' {
+    // BBGTOOLS:DEEPCSA:SIGNATURESNONPROT:SIGPROFILERASSIGNMENT
+    withName: 'SIGPROFILERASSIGNMENT' {
         memory = { 2.GB * task.attempt }
     }
 
@@ -127,7 +114,7 @@ process {
         memory = { 4.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:MUTATEDCELLSVAF:MUTATEDGENOMESFROMVAFAM' {
+    withName: 'MUTATEDGENOMESFROMVAFAM' {
         errorStrategy = 'ignore'
         maxRetries = 1
     }
@@ -145,7 +132,7 @@ process {
         memory = { 30.GB * task.attempt }
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:FILTERNANOSEQSNP' {
+    withName: 'FILTERNANOSEQSNP' {
         memory = { 8.GB * task.attempt }
     }
 

conf/exome.config

@@ -93,17 +93,14 @@ process {
 
 
 
-    withName: '(BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:SOMATICMUTATIONS*|BBGTOOLS:DEEPCSA:OMEGANONPROT.*:SUBSETPANEL*)' {
+    withName: 'BBGTOOLS:DEEPCSA:MUT_PREPROCESSING:SOMATICMUTATIONS*' {
         cpus   = { 2 * task.attempt }
         memory = { 4.GB * task.attempt }
         time   = { 360.min * task.attempt }
     }
-
-    withName: 'BBGTOOLS:DEEPCSA:MUTRATE.*:MUTRATE*' {
-        memory = { 8.GB * task.attempt }
-    }
-
-    withName: '(BBGTOOLS:DEEPCSA:OMEGA.*:(PREPROCESSING|ESTIMATOR).*|BBGTOOLS:DEEPCSA:MULTIQC)' {
+
+    // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING
+    withName: 'PREPROCESSING|ESTIMATOR|BBGTOOLS:DEEPCSA:MULTIQC' {
         memory = { 4.GB * task.attempt }
     }
 

conf/modules.config

@@ -132,22 +132,11 @@ process {
         ]
     }
 
-    withName: SUBSETPILEUP {
-        ext.prefix    = { ".subset_pileup" }
-        ext.args      = ''
-        ext.args2     = '-s 1 -b 2 -e 2'
-        ext.args3     = '-h'
-        ext.extension = 'tsv'
-        ext.header    = 'pile'
-        publishDir    = [
-            enabled: false
-        ]
-    }
-
     withName: 'BBGTOOLS:DEEPCSA:.*ALL:.*' {
         ext.prefix = { ".all" }
     }
 
+    // Gated by params.profileintrons; "no matching selector" warning is expected when the feature is off
     withName: 'BBGTOOLS:DEEPCSA:.*INTRONS:.*' {
         ext.prefix = { ".introns" }
     }
@@ -415,6 +404,7 @@ process {
         ]
     }
 
+    // Gated by params.profilenonprot; "no matching selector" warning is expected when the feature is off
     withName: '.*NONPROT:SUBSETMUTPROFILE' {
         ext.filters    = {
             [
@@ -569,13 +559,6 @@ process {
         ]
     }
 
-    withName: READSPOSBED {
-        ext.tool   = "readsxposition"
-        publishDir = [
-            enabled: false
-        ]
-    }
-
     withName: ONCODRIVECLUSTL {
         ext.args = "-sim region_restricted \
                             -kmer 3 \
@@ -650,7 +633,7 @@ process {
     }
 
     // BBGRegressions output configuration
-    withName: '.*:REGRESSIONS.*:EDITCONFIG' {
+    withName: 'EDITCONFIG' {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -661,7 +644,8 @@ process {
         ]
     }
 
-    withName: '.*:REGRESSIONS.*:CREATE_INPUT' {
+    // REGRESSIONS:CREATE_INPUT
+    withName: 'CREATE_INPUT' {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -672,7 +656,8 @@ process {
         ]
     }
 
-    withName: '.*:REGRESSIONS.*:MODELS' {
+    // REGRESSIONS:MODELS
+    withName: 'MODELS' {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -682,7 +667,8 @@ process {
         ]
     }
 
-    withName: '.*:REGRESSIONS.*:PLOT' {
+    // REGRESSIONS:PLOT
+    withName: 'PLOT' {
         publishDir = [
             [
                 mode: params.publish_dir_mode,

conf/tmp_quick_fixes.config

@@ -15,11 +15,12 @@ process {
         errorStrategy = 'ignore'
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:MUTATEDCELLSVAF:MUTATEDGENOMESFROMVAFAM' {
+    withName: 'MUTATEDGENOMESFROMVAFAM' {
         errorStrategy = 'ignore'
         maxRetries = 1
     }
 
+    // Gated by params.expected_mutated_cells; "no matching selector" warning is expected when the feature is off
     withName: "BBGTOOLS:DEEPCSA:EXPECTEDMUTATEDCELLS:.*" {
         errorStrategy = 'ignore'
         maxRetries = 1

conf/tools/omega.config

@@ -73,6 +73,7 @@ process {
         ext.prefix = { ".multi" }
     }
 
+    // Gated by params.profilenonprot && params.positive_selection_non_protein_affecting && params.omega_multi; "no matching selector" warning is expected when the feature is off
     withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROTMULTI:.*' {
         ext.prefix = { ".non_prot_aff.multi" }
     }
@@ -86,6 +87,7 @@ process {
         ext.prefix = { ".multi.global_loc" }
     }
 
+    // Gated by params.omega_globalloc (+ params.profilenonprot && params.positive_selection_non_protein_affecting); "no matching selector" warning is expected when the feature is off
     withName: 'BBGTOOLS:DEEPCSA:OMEGANONPROT:.*GLOBALLOC' {
         ext.prefix = { ".non_prot_aff.global_loc" }
     }
@@ -106,6 +108,7 @@ process {
         ]
     }
 
+    // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR
     withName: ESTIMATOR {
         ext.option = 'mle'
         ext.args   = ""
@@ -185,8 +188,8 @@ process {
         ]
     }
 
-
-    withName: 'PREPROCESSING.*|ESTIMATOR.*' {
+    // BBGTOOLS:DEEPCSA:OMEGA:ESTIMATOR and BBGTOOLS:DEEPCSA:OMEGA:PREPROCESSING
+    withName: 'PREPROCESSING|ESTIMATOR' {
         ext.assembly = params.vep_genome == 'GRCh38'
             ? 'hg38'
             : params.vep_genome == 'GRCm39'

conf/tools/panels.config

@@ -57,67 +57,7 @@ process {
         ]
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSALL' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelsall" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSPROTAFFECT' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelsprotaffect" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSNONPROTAFFECT' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelsnonprotaffect" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSEXONS' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelsexons" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSINTRONS' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelsintrons" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:CREATEPANELS:CREATESAMPLEPANELSSYNONYMOUS' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/samplepanels/createsamplepanelssynonymous" },
-                pattern: "*{tsv,bed}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSALL' {
+    withName: 'EXPANDREGIONSALL|EXPANDREGIONSNONPROT|EXPANDREGIONSPROT|EXPANDREGIONSSYNONYMOUS|EXPANDREGIONSEXONS' {
         publishDir = [
             [
                 mode: params.publish_dir_mode,
@@ -127,43 +67,4 @@ process {
         ]
     }
 
-    withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSNONPROT' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/expandedregions/" },
-                pattern: "*{tsv,json}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSPROT' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/expandedregions/" },
-                pattern: "*{tsv,json}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSSYNONYMOUS' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/expandedregions/" },
-                pattern: "*{tsv,json}",
-            ]
-        ]
-    }
-
-    withName: 'BBGTOOLS:DEEPCSA:ENRICHPANELS:EXPANDREGIONSEXONS' {
-        publishDir = [
-            [
-                mode: params.publish_dir_mode,
-                path: { "${params.outdir}/regions/expandedregions/" },
-                pattern: "*{tsv,json}",
-            ]
-        ]
-    }
 }