Merge pull request #70 from maxibor/dev

Fix Spades memory conversion issue

CHANGELOG.md

@@ -26,6 +26,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Fixed channel joining for multiple samples causing MetaBAT2 error [#32](https://github.com/nf-core/mag/issues/32)
 - Update MetaBAT2 from v2.13 to v2.15
 - Fix number of threads used by MetaBAT2 program `jgi_summarize_bam_contig_depths`
+- Fix SPAdes memory conversion issue [#70](https://github.com/nf-core/mag/pull/70)
 - No more ignoring errors in SPAdes assembly
 
 ### `Deprecated`

main.nf

@@ -944,12 +944,12 @@ process spadeshybrid {
     params.manifest && !params.single_end && !params.skip_spadeshybrid
 
     script:
-    def maxmem = "${task.memory.toString().replaceAll(/[\sGB]/,'')}"
+    maxmem = task.memory.toGiga()
     if ( !params.spadeshyrid_fix_cpus || task.cpus == params.spadeshybrid_fix_cpus )
         """
         metaspades.py \
             --threads "${task.cpus}" \
-            --memory "$maxmem" \
+            --memory $maxmem \
             --pe1-1 ${sr[0]} \
             --pe1-2 ${sr[1]} \
             --nanopore ${lr} \
@@ -987,12 +987,12 @@ process spades {
     !params.single_end && !params.skip_spades
 
     script:
-    def maxmem = "${task.memory.toString().replaceAll(/[\sGB]/,'')}"
+    maxmem = task.memory.toGiga()
     if ( !params.spades_fix_cpus || task.cpus == params.spades_fix_cpus )
         """
         metaspades.py \
             --threads "${task.cpus}" \
-            --memory "$maxmem" \
+            --memory $maxmem \
             --pe1-1 ${sr[0]} \
             --pe1-2 ${sr[1]} \
             -o spades