Merge branch 'dev' into dp24_yaml_update

sanger-tol · Nov 22, 2023 · 60f129f · 60f129f
2 parents fd73077 + f6b94a7
commit 60f129f
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Showing 10 changed files with 154 additions and 128 deletions.
diff --git a/README.md b/README.md
@@ -80,7 +80,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 <!--TODO: Citation-->
 
-If you use sanger-tol/treeval for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX).
+If you use sanger-tol/treeval for your analysis, please cite it using the following doi: [10.5281/zenodo.10047653](https://doi.org/10.5281/zenodo.10047653).
 
 ### Tools
 

diff --git a/conf/base.config b/conf/base.config
@@ -66,15 +66,21 @@ process {
     }
 
     // CUSTOM CONFIGS
-    // TODO: add process.tiny
+
+    withLabel:process_tiny {
+        cpus   = { check_max( 1                         , 'cpus'    ) }
+        memory = { check_max( 100.MB    * task.attempt  , 'memory'  ) }
+        time   = { check_max( 4.h       * task.attempt  , 'time'    ) }
+    }
 
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
 
+    // IN CASES WHERE THERE IS ONE HIC FILE THIS WILL NEED ALMOST NOTHING
     withName:SAMTOOLS_MERGE {
-        cpus    = { check_max( 16       * 1, 'cpus'  ) }
-        memory  = { check_max( 150.GB    * task.attempt, 'memory') }
+        cpus    = { check_max( 16        * 1, 'cpus'  ) }
+        memory  = { check_max( 50.GB     * task.attempt, 'memory') }
     }
 
     // RESOURCES: MEMORY INTENSIVE STEPS, SOFTWARE TO BE UPDATED TO COMBAT THIS
@@ -151,6 +157,12 @@ process {
         memory  = { check_max( 100.MB   * task.attempt, 'memory' ) }
     }
 
+    withName: SNAPSHOT_SRES {
+        cpus    = { check_max( 1        * task.attempt, 'cpus'   ) }
+        memory  = { check_max( 1.GB     * task.attempt, 'memory' ) }
+    }
+
+    // NOT CURRENTLY IN USE
     withName: SNAPSHOT_HRES {
         cpus    = { check_max( 1      * task.attempt, 'cpus'   ) }
         memory  = { check_max( 50.GB  * task.attempt, 'memory' ) }
@@ -173,7 +185,7 @@ process {
 
     withName: COOLER_CLOAD {
         cpus   = { check_max( 16     * 1, 'cpus'    ) }
-        memory = { check_max( 100.GB * task.attempt, 'memory'  ) }
+        memory = { check_max( 50.GB * task.attempt, 'memory'  ) }
     }
 
     withName: BUSCO {