Fixed checkpoint error: snakemake/snakemake#1930, snakemake/snakemake…

…#823
ThomasBrazier · Apr 5, 2024 · 6a50038 · 6a50038
1 parent ce185e2
commit 6a50038
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/workflow/rules/fastq2bam.smk b/workflow/rules/fastq2bam.smk
@@ -43,8 +43,8 @@ rule dedup:
     input:
         unpack(dedup_input)
     output:
-        dedupBam = temp("results/{refGenome}/bams/{sample}_final.bam"),
-        dedupBai = temp("results/{refGenome}/bams/{sample}_final.bam.bai")
+        dedupBam = "results/{refGenome}/bams/{sample}_final.bam",
+        dedupBai = "results/{refGenome}/bams/{sample}_final.bam.bai"
     conda:
         "../envs/sambamba.yml"
     resources:

diff --git a/workflow/rules/intervals.smk b/workflow/rules/intervals.smk
@@ -66,7 +66,9 @@ checkpoint create_gvcf_intervals:
         ref = "results/{refGenome}/data/genome/{refGenome}.fna",
         fai = "results/{refGenome}/data/genome/{refGenome}.fna.fai",
         dictf = "results/{refGenome}/data/genome/{refGenome}.dict",
-        intervals = "results/{refGenome}/intervals/master_interval_list.list"
+        intervals = "results/{refGenome}/intervals/master_interval_list.list",
+        dedupBam = "results/{refGenome}/bams/{sample}_final.bam",
+        dedupBai = "results/{refGenome}/bams/{sample}_final.bam.bai"
     output:
         fof = "results/{refGenome}/intervals/gvcf_intervals/intervals.txt",
         out_dir = directory("results/{refGenome}/intervals/gvcf_intervals"),