Merge pull request #37 from hoelzer-lab/raxml-cpu-issue

add auto option for RAXML-NG max CPUs on HPC, hopefully also works local…
hoelzer-lab · Apr 27, 2022 · a4787d2 · a4787d2
2 parents 719d94d + 58538b7
commit a4787d2
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/modules/raxml.nf b/modules/raxml.nf
@@ -2,7 +2,7 @@
 
 process raxml {
   label 'raxml'
-  publishDir "${params.output}/raxml", mode: 'copy', pattern: "*.aa" 
+  publishDir "${params.output}/raxml", mode: 'copy', pattern: "*.support" 
 
   input: 
     file(aln)
@@ -13,7 +13,8 @@ process raxml {
   script:
     """
     #raxmlHPC-PTHREADS-SSE3 -T ${task.cpus} -f a -x 1234 -p 1234 -s ${aln} -n aa -m PROTGAMMAWAG -N ${params.bootstrap}
-    raxml-ng --all --threads ${task.cpus} --msa ${aln} --prefix coreGenome_mafft --msa-format FASTA --model PROTGTR+G --bs-trees ${params.bootstrap} 
+    raxml-ng --all --threads auto{${task.cpus}} --msa ${aln} --prefix coreGenome_mafft --msa-format FASTA --model PROTGTR+G --bs-trees ${params.bootstrap} 
     """
 }
 
+// --threads auto{4} defined based on https://github.com/amkozlov/raxml-ng/wiki/Parallelization#core-oversubscription and bc/ error on SLURM HPC