Merge branch 'CW-3551' into 'dev'

reduce max memory requested by 1 GB to not fail in WSL or the cloud [CW-3551]

Closes CW-3551

See merge request epi2melabs/workflows/wf-alignment!128

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v1.1.1]
+### Changed
+- Reduced the memory requested by some processes to avoid failing in WSL (since there is slightly less memory available in WSL than specified in `.wslconfig`).
+
 ## [v1.1.0]
 ### Changed
 - Some formatting changes to github issue template.

main.nf

@@ -19,7 +19,7 @@ process makeMMIndex {
     cpus params.threads
     memory {
         def ref_size = combined_refs.size()
-        combined_refs.size() > 1e9 ? "32 GB" : "12 GB"
+        combined_refs.size() > 1e9 ? "31 GB" : "11 GB"
     }
     input:
         path combined_refs, stageAs: "combined_references.fasta"
@@ -38,7 +38,7 @@ process checkReferences {
     cpus params.threads
     memory {
         def ref_size = combined_refs.size()
-        combined_refs.size() > 1e9 ? "32 GB" : "12 GB"
+        combined_refs.size() > 1e9 ? "31 GB" : "11 GB"
     }
     input:
         path "combined_references.mmi"
@@ -57,7 +57,7 @@ process alignReads {
     label "wfalignment"
     cpus params.threads
     memory {
-        combined_refs.size() > 1e9 ? "32 GB" : "12 GB"
+        combined_refs.size() > 1e9 ? "31 GB" : "11 GB"
     }
     input:
         tuple val(meta), path(input)
@@ -135,7 +135,7 @@ process readDepthPerRef {
     // TODO: check if parallelisation with `xargs` or `parallel` is more efficient
     label "wfalignment"
     cpus 3
-    memory "8 GB"
+    memory "7 GB"
     input:
         tuple val(meta), path(alignment), path(index)
         path ref_len
@@ -161,7 +161,7 @@ process readDepthPerRef {
 process makeReport {
     label "wfalignment"
     cpus 1
-    memory "12 GB"
+    memory "11 GB"
     input:
         path "readstats/*"
         path "flagstat/*"
@@ -345,7 +345,7 @@ process output {
 process configure_jbrowse {
     label "wfalignment"
     cpus 1
-    memory { reference.size() > 1e9 ? "16 GB" : "2 GB" }
+    memory { reference.size() > 1e9 ? "15 GB" : "2 GB" }
     input:
         path(alignments)
         path(indexes)

nextflow.config

@@ -52,7 +52,7 @@ manifest {
     description     = 'Align Nanopore reads and visualize mapping statistics.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=23.04.2'
-    version         = 'v1.1.0'
+    version         = 'v1.1.1'
 }
 
 epi2melabs {

subworkflows/process_references.nf

@@ -23,7 +23,7 @@ process combine {
 process fx2tab {
     label "wfalignment"
     cpus 1
-    memory { reference.size() > 1e9 ? "16 GB" : "2 GB" }
+    memory { reference.size() > 1e9 ? "15 GB" : "2 GB" }
     input:
         path reference
     output: