Merge pull request #672 from maxplanck-ie/dev_wd

Alevin downscale threads + specify mem
maxplanck-ie · Aug 21, 2020 · cfb3597 · cfb3597
2 parents dec4593 + fb3899d
commit cfb3597
Show file tree

Hide file tree

Showing 2 changed files with 3 additions and 1 deletion.
diff --git a/snakePipes/shared/rules/scRNAseq_Alevin.snakefile b/snakePipes/shared/rules/scRNAseq_Alevin.snakefile
@@ -29,7 +29,7 @@ rule SalmonAlevin:
             err = "Alevin/logs/alevin.{sample}.err"
         #Use RNAseq env because Salmon already installed there (no need for duplication).
         conda: CONDA_RNASEQ_ENV
-        threads: 40
+        threads: 8
         shell:"""
             salmon alevin -l {params.libtype} -1 {input.R1} -2 {input.R2} {params.protocol} -i Salmon/SalmonIndex -p {threads} -o {params.outdir} --tgMap {params.tgMap} --dumpFeatures --dumpMtx --numCellBootstraps 100 > {log.out} 2> {log.err}
             """

diff --git a/snakePipes/workflows/scRNAseq/cluster.yaml b/snakePipes/workflows/scRNAseq/cluster.yaml
@@ -18,6 +18,8 @@ filter_cells_raceid:
     memory: 12G
 STARsolo:
     memory: 6G
+SalmonAlevin:
+    memory: 6G
 cellsort_bam:
     memory: 10G
 velocyto: