Sorted modules.config, closes #98

sanger-tol · Nov 23, 2023 · fea3abc · fea3abc
1 parent 0c75047
commit fea3abc
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Showing 2 changed files with 60 additions and 24 deletions.
diff --git a/conf/base.config b/conf/base.config
@@ -67,6 +67,7 @@ process {
 
     // CUSTOM CONFIGS
 
+    // NOTE: For processes that grab files or generate csv
     withLabel:process_tiny {
         cpus   = { check_max( 1                         , 'cpus'    ) }
         memory = { check_max( 100.MB    * task.attempt  , 'memory'  ) }
@@ -110,7 +111,7 @@ process {
         time    = { check_max( 20.h     * task.attempt, 'time'      ) }
     }
 
-// For Large complex genomes > 4Gb
+    // For Large complex genomes > 4Gb
     //withName: '.*:.*:LONGREAD_COVERAGE:(MINIMAP2_ALIGN|MINIMAP2_ALIGN_SPLIT)' {
     //    cpus    = { check_max( 20       * 1, 'cpus'                 ) }
     //    memory  = { check_max( 400.GB   * task.attempt, 'memory'    ) }
@@ -184,12 +185,12 @@ process {
     }
 
     withName: COOLER_CLOAD {
-        cpus   = { check_max( 16     * 1, 'cpus'    ) }
-        memory = { check_max( 50.GB * task.attempt, 'memory'  ) }
+        cpus   = { check_max( 16    * 1, 'cpus'    ) }
+        memory = { check_max( 6.GB  * task.attempt, 'memory'  ) }
     }
 
     withName: BUSCO {
-        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }
+        cpus   = { check_max( 16    * task.attempt, 'cpus'    ) }
         memory = { check_max( 50.GB * task.attempt, 'memory'  ) }
         time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }

diff --git a/conf/modules.config b/conf/modules.config
@@ -57,12 +57,29 @@ process {
         ]
     }
 
+    //
     // MODULE CONFIGS
+    //
 
+    //
+    // SUBWORKFLOW: MULTIPLE SUBWORKFLOWS
+    //
     withName: BEDTOOLS_SORT {
         ext.prefix      = { "${meta.id}.sorted" }
     }
 
+
+    //
+    // SUBWORKFLOW: SELFCOMP
+    //
+    withName : MUMMER {
+        ext.args        = "-n -b -c -L -l 400"
+    }
+
+
+    //
+    // SUBWORKFLOW: REPEAT_DENSITY
+    //
     withName: GNU_SORT_A {
         ext.args        = { "-k1,1 -k2,2n -S${task.memory.mega - 100}M -T ." }
         ext.suffix      = { "intersect" }
@@ -91,11 +108,31 @@ process {
         ext.args        = { "-c 4 -o sum" }
     }
 
+    withName: ".*:.*:REPEAT_DENSITY:UCSC_BEDGRAPHTOBIGWIG" {
+        ext.prefix      = { "${meta.id}_repeat_density" }
+    }
+
+    withName: ".*:.*:REPEAT_DENSITY:REFORMAT_INTERSECT" {
+        ext.prefix      = { "${meta.id}_repeat_mk" }
+    }
+
+
+    //
+    // SUBWORKFLOW: GAP_FINDER
+    //
     withName: SEQTK_CUTN {
         ext.args        = "-n 1"
         ext.prefix      = { "${meta.id}_gap" }
     }
 
+    withName: ".*:.*:GAP_FINDER:TABIX_BGZIPTABIX" {
+        ext.prefix      = { "gap_${meta.id}" }
+    }
+
+
+    //
+    // SUBWORKFLOW: GENE ALIGNMENTS
+    //
     withName: MINIPROT_ALIGN {
         ext.args        = " --gff -j1 -ut16 --gff-delim='#' "
     }
@@ -117,39 +154,32 @@ process {
         ext.prefix      = { "${meta.id}_prot" }
     }
 
+
+    //
+    // SUBWORKFLOW: INSILICO_DIGEST
+    //
     withName: ".*:.*:INSILICO_DIGEST:UCSC_BEDTOBIGBED" {
         ext.args        = { "-type=bed4+1 -extraIndex=length" }
         ext.prefix      = { "${meta.id}" }
     }
 
+
+    //
+    // SUBWORKFLOW: SYNTENY
+    //
     withName: ".*:.*:SELFCOMP:UCSC_BEDTOBIGBED" {
         ext.args        = { " -type=bed3+3 -extraIndex=qName,qStart,qEnd" }
         ext.prefix      = { "${meta.id}_selfcomp" }
     }
 
-    withName: ".*:.*:REPEAT_DENSITY:UCSC_BEDGRAPHTOBIGWIG" {
-        ext.prefix      = { "${meta.id}_repeat_density" }
-    }
-
-    withName: ".*:.*:REPEAT_DENSITY:REFORMAT_INTERSECT" {
-        ext.prefix      = { "${meta.id}_repeat_mk" }
-    }
-
-    withName: ".*:.*:GAP_FINDER:TABIX_BGZIPTABIX" {
-        ext.prefix      = { "gap_${meta.id}" }
-    }
-
     withName: ".*:.*:SYNTENY:MINIMAP2_ALIGN" {
         ext.args        = "-t 8 -x asm10"
         ext.prefix      = { "${meta.id}_synteny_${reference.getName().tokenize(".")[0]}" }
     }
 
-    withName : MUMMER {
-        ext.args        = "-n -b -c -L -l 400"
-    }
 
     //
-    // LONGREAD BLOCK
+    // SUBWORKFLOW: LONGREAD
     //
     withName: ".*:.*:LONGREAD_COVERAGE:MINIMAP2_ALIGN" {
             ext.args    = "--MD -t 8"
@@ -202,8 +232,9 @@ process {
         ext.prefix      = { "${meta.id}_coverage_log" }
     }
 
+
     //
-    // TELOMERE BLOCK
+    // SUBWORKFLOW: TELOMERE
     //
     withName: "FIND_TELOMERE_REGIONS" {
         ext.find_telomere       = "find_telomere"
@@ -218,8 +249,9 @@ process {
         ext.prefix      = { "telo_${meta.id}" }
     }
 
+
     //
-    // BUSCO BLOCK
+    // SUBWORKFLOW: BUSCO
     //
     withName: ".*:.*:BUSCO_ANNOTATION:UCSC_BEDTOBIGBED" {
         ext.args        = { "-type=bed3+4 -extraIndex=name,OrthoDBurl" }
@@ -243,9 +275,11 @@ process {
         ext.args        = "--mode genome"
     }
 
+
     //
-    // HIC MAPPING BLOCK
+    // SUBWORKFLOW: HIC MAPPING
     // normal = standard run, pi = "pre-ingestion", hr = High res
+    //
     withName: PRETEXTMAP_STANDRD {
         ext.args        = "--sortby length --mapq 0"
         ext.prefix      = { "${meta.id}_normal_pi" }
@@ -307,8 +341,9 @@ process {
         ext.args        = { "-k2,2 -nr -S${task.memory.mega - 100}M -T ." }
     }
 
+
     //
-    // KMER
+    // SUBWORKFLOW: KMER
     //
     withName: CAT_CAT {
         ext.prefix      = { "${meta.id}_merged.fasta.gz" }