Merge pull request #284 from nf-core/fix-time-limits

Fix time limits

Author: grst

CHANGELOG.md

@@ -7,7 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279))
 - Add support for paired GEX+ATAC sequencing using cellranger-arc ([#274](https://github.com/nf-core/scrnaseq/pull/274))
-- Increase default runtime limits for all processes ([#281])(https://github.com/nf-core/scrnaseq/pull/281)
+- Increase default runtime limits for some processes ([#281](https://github.com/nf-core/scrnaseq/pull/281), [#284](https://github.com/nf-core/scrnaseq/pull/284))
 - Better support for custom protocols ([#273](https://github.com/nf-core/scrnaseq/pull/273)).
   - The universc protocol is now specified via the `--protocol` flag
   - Any protocol specified is now passed to the respective aligner

conf/base.config

@@ -27,25 +27,25 @@ process {
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 6.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h  * task.attempt, 'time'    ) }
+        time   = { check_max( 4.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_low {
         cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }
         memory = { check_max( 12.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
+        time   = { check_max( 4.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_medium {
         cpus   = { check_max( 6     * task.attempt, 'cpus'    ) }
         memory = { check_max( 36.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 120.h   * task.attempt, 'time'  ) }
+        time   = { check_max( 8.h   * task.attempt, 'time'    ) }
     }
     withLabel:process_high {
         cpus   = { check_max( 12    * task.attempt, 'cpus'    ) }
         memory = { check_max( 72.GB * task.attempt, 'memory'  ) }
-        time   = { check_max( 240.h * task.attempt, 'time'    ) }
+        time   = { check_max( 16.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_long {
-        time   = { check_max( 240.h * task.attempt, 'time'    ) }
+        time   = { check_max( 20.h  * task.attempt, 'time'    ) }
     }
     withLabel:process_high_memory {
         memory = { check_max( 200.GB * task.attempt, 'memory' ) }
@@ -60,8 +60,4 @@ process {
     withName:CUSTOM_DUMPSOFTWAREVERSIONS {
         cache = false
     }
-    //Fix for issue 196
-    withName: 'NFCORE_SCRNASEQ:SCRNASEQ:SCRNASEQ_ALEVIN:ALEVINQC' {
-        time = '20.h'
-    }
 }

conf/modules.config

@@ -17,6 +17,10 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+    withName: FASTQC {
+        time   = { check_max( 120.h  * task.attempt, 'time'    ) }
+    }
+
     withName: SAMPLESHEET_CHECK {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },
@@ -79,6 +83,7 @@ if(params.aligner == "cellranger") {
                 mode: params.publish_dir_mode
             ]
             ext.args = {"--chemistry ${meta.chemistry} " + (meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : '')}
+            time   = { check_max( 240.h  * task.attempt, 'time'    ) }
         }
     }
 }
@@ -105,6 +110,7 @@ if(params.aligner == "cellrangerarc") {
                 mode: params.publish_dir_mode
             ]
             ext.args = {meta.expected_cells ? "--expect-cells ${meta.expected_cells}" : ''}
+            time   = { check_max( 240.h  * task.attempt, 'time'    ) }
         }
     }
 }
@@ -134,6 +140,7 @@ if(params.aligner == "universc") {
                 path: "${params.outdir}/universc",
                 mode: params.publish_dir_mode
             ]
+            time   = { check_max( 240.h  * task.attempt, 'time'    ) }
         }
     }
 }
@@ -159,6 +166,10 @@ if (params.aligner == "alevin") {
             ]
             ext.args = "-r cr-like"
         }
+        //Fix for issue 196
+        withName: 'ALEVINQC' {
+            time = '120.h'
+        }
     }
 }