Merge pull request #154 from sanger-tol/patch

More memory for crumble !

Author: muffato

CHANGELOG.md

@@ -3,6 +3,12 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [[1.3.4](https://github.com/sanger-tol/readmapping/releases/tag/1.3.4)] - Antipodean Opaleye (patch 4) - [2025-03-18]
+
+### Enhancements & fixes
+
+- Even more memory for CRUMBLE
+
 ## [[1.3.3](https://github.com/sanger-tol/readmapping/releases/tag/1.3.3)] - Antipodean Opaleye (patch 3) - [2025-02-10]
 
 ### Enhancements & fixes

CITATION.cff

@@ -0,0 +1,42 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: sanger-tol/readmapping v1.3.4
+type: software
+authors:
+    - given-names: Sandra Ruth
+      family-names: Babirye
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0009-0004-7773-7008"
+    - given-names: Tyler
+      family-names: Chafin
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0001-8687-5905"
+    - given-names: Chau
+      family-names: Duong
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0009-0001-0649-2291"
+    - given-names: Matthieu
+      family-names: Muffato
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7860-3560"
+    - given-names: Guoying
+      family-names: Qi
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-1262-8973"
+    - given-names: Priyanka
+      family-names: Surana
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0002-7167-0875"
+    - given-names: Bethan
+      family-names: Yates
+      affiliation: Wellcome Sanger Institute
+      orcid: "https://orcid.org/0000-0003-1658-1762"
+identifiers:
+    - type: doi
+      value: 10.5281/zenodo.6563577
+repository-code: "https://github.com/sanger-tol/readmapping"
+license: MIT
+version: 1.3.4
+date-released: "2022-10-07"

conf/base.config

@@ -105,9 +105,7 @@ process {
 
     withName: CRUMBLE {
         // Most genomes seem happy with 1 GB, but some need a bit more, and others a lot more.
-        // There is a weak, but existing, correlation between memory usage and the number of reads.
-        // The formula below is a quadratic growth based on the attempt number.
-        memory = { check_max( task.attempt * (task.attempt + 1) * 512.MB * Math.ceil( meta.read_count / 1000000000 ), 'memory' ) }
+        memory = { check_max( 1.GB * Math.pow(3, task.attempt-1), 'memory' ) }
         // 100k reads per hour for PacBio, 50m for HiC
         time   = { check_max( 1.h  * Math.ceil( meta.read_count / (meta.datatype == "pacbio" ? 100000 : 50000000)) * task.attempt, 'time'   ) }
     }

nextflow.config

@@ -232,7 +232,7 @@ manifest {
     description     = 'Pipeline to map reads generated using different sequencing technologies against a genome assembly.'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '1.3.3'
+    version         = '1.3.4'
     doi             = '10.5281/zenodo.6563577'
 }