Merge branch 'master' into develop

genxnetwork · Jan 12, 2023 · 80ca645 · 80ca645
2 parents 8f16591 + 599fcd6
commit 80ca645
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/rules/imputation.smk b/rules/imputation.smk
@@ -135,5 +135,5 @@ rule merge_convert_imputed_to_plink:
         '''
         # please mind a merge step in merge_imputation_filter for germline
         plink --vcf {input} --make-bed --out {params.out} | tee {log}
-        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{batch}_merged_imputed |& tee {log}
+        plink --bfile {params.background} --bmerge {params.out} --make-bed --out plink/{wildcards.batch}_merged_imputed |& tee {log}
         '''
diff --git a/rules/preprocessing.smk b/rules/preprocessing.smk
@@ -109,7 +109,7 @@ if assembly == 'hg38':
             mem_mb=_mem_gb_for_ram_hungry_jobs() * 1024
         shell:
             '''
-               java -Xmx{params.mem_gb}g -jar /picard/picard.jar LiftoverVcf WARN_ON_MISSING_CONTIG=true MAX_RECORDS_IN_RAM=5000 I={input.vcf} O={output.vcf} CHAIN={LIFT_CHAIN} REJECT=vcf/chr{wildcards.batch}_rejected.vcf.gz R={GRCH37_FASTA} |& tee -a {log}
+               picard -Xmx{params.mem_gb}g LiftoverVcf -WARN_ON_MISSING_CONTIG true -MAX_RECORDS_IN_RAM 5000 -I {input.vcf} -O {output.vcf} -CHAIN {LIFT_CHAIN} -REJECT vcf/chr{wildcards.batch}_rejected.vcf.gz -R {GRCH37_FASTA} |& tee -a {log}
             '''
 else:
     rule copy_liftover: