Relaxed mem as well

naobservatory · Nov 20, 2024 · 914cd04 · 914cd04
1 parent de9cc5a
commit 914cd04
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/modules/local/bbmap/main.nf b/modules/local/bbmap/main.nf
@@ -22,7 +22,7 @@ process BBMAP {
         stats=!{sample}_!{suffix}_bbmap.stats.txt
         io="in=${in1} in2=${in2} outu=${ou1} outu2=${ou2} outm=${om1} outm2=${om2} statsfile=${stats} path=!{index_dir}"
         # Define parameters
-        par="minid=0.8 maxindel=4 bwr=0.25 bw=25 quickmatch minhits=2 t=!{task.cpus} -Xmx60g"
+        par="minid=0.8 maxindel=4 bwr=0.25 bw=25 quickmatch minhits=2 t=!{task.cpus} -Xmx!{task.memory.toGiga()}g"
         # Execute
         bbmap.sh ${io} ${par}
         '''

diff --git a/modules/local/clumpify/main.nf b/modules/local/clumpify/main.nf
@@ -16,7 +16,7 @@ process CLUMPIFY_PAIRED {
         op2=!{sample}_dedup_2.fastq.gz
         io="in=${in1} in2=${in2} out=${op1} out2=${op2}"
         # Define parameters
-        par="reorder dedupe passes=6 addcount=t t=!{task.cpus} -Xmx30g"
+        par="reorder dedupe passes=6 addcount=t t=!{task.cpus} -Xmx!{task.memory.toGiga()}g"
         # Execute
         clumpify.sh ${io} ${par}
         '''
@@ -38,7 +38,7 @@ process CLUMPIFY_SINGLE {
         out=!{sample}_dedup.fastq.gz
         io="in=${in} out=${out}"
         # Define parameters
-        par="reorder dedupe rcomp passes=6 addcount=t t=!{task.cpus} -Xmx30g"
+        par="reorder dedupe rcomp passes=6 addcount=t t=!{task.cpus} -Xmx!{task.memory.toGiga()}g"
         # Execute
         clumpify.sh ${io} ${par}
         '''