Specify threads in rule

NBISweden · Jun 17, 2024 · e6598cc · e6598cc
1 parent 57f3ba5
commit e6598cc
Show file tree

Hide file tree

Showing 3 changed files with 4 additions and 1 deletion.
diff --git a/config/slurm/profile/config_plugin_dardel.yaml b/config/slurm/profile/config_plugin_dardel.yaml
@@ -90,6 +90,7 @@ set-threads:
   - filter_biallelic_missing_vcf=48
 ### PCA
   - vcf2plink_pca=16
+  - plink_eigenvec=8
 ### runs of homozygosity
   - filter_vcf_hwe=16
   - vcf2plink_hwe=16

diff --git a/config/slurm/profile/config_plugin_rackham.yaml b/config/slurm/profile/config_plugin_rackham.yaml
@@ -86,6 +86,7 @@ set-threads:
   - filter_biallelic_missing_vcf=6
 ### PCA
   - vcf2plink_pca=2
+  - plink_eigenvec=1
 ### runs of homozygosity
   - filter_vcf_hwe=2
   - vcf2plink_hwe=2

diff --git a/workflow/rules/10_pca.smk b/workflow/rules/10_pca.smk
@@ -66,6 +66,7 @@ rule plink_eigenvec:
     output:
         eigenvec="results/{dataset}/pca/" + REF_NAME + ".{dataset}.merged.biallelic.fmissing{fmiss}.{chr}.eigenvec",
         eigenval="results/{dataset}/pca/" + REF_NAME + ".{dataset}.merged.biallelic.fmissing{fmiss}.{chr}.eigenval",
+    threads: 1
     params:
         bfile="results/{dataset}/pca/" + REF_NAME + ".{dataset}.merged.biallelic.fmissing{fmiss}.{chr}",
     log:
@@ -77,7 +78,7 @@ rule plink_eigenvec:
         samples=`cat {input.fam} | wc -l`
         if [ "$samples" -gt 1 ]
         then
-          plink --bfile {params.bfile} --allow-extra-chr --pca --out {params.bfile} 2> {log}
+          plink --bfile {params.bfile} --threads {threads} --allow-extra-chr --pca --out {params.bfile} 2> {log}
         else
           touch {output.eigenvec} && touch {output.eigenval} 2> {log}
           echo "Not enough samples to calculate a PCA." >> {log}