Updating GH actions, small fixes for v8 upgrade

friendsofstrandseq · Jun 20, 2024 · 586651d · 586651d
1 parent 74ef4a9
commit 586651d
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 1 deletion.
diff --git a/workflow/rules/regenotyping.smk b/workflow/rules/regenotyping.smk
@@ -7,6 +7,7 @@ rule mergeBams:
         bam=selected_input_bam,
         bai=selected_input_bai,
         labels="{folder}/{sample}/cell_selection/labels.tsv",
+        ploidy_summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
     output:
         temp("{folder}/{sample}/merged_bam/merged.raw.bam"),
     log:
@@ -62,7 +63,6 @@ rule regenotype_SNVs:
         fasta_index="{fasta}.fai".format(
             fasta=config["references_data"][config["reference"]]["reference_fasta"]
         ),
-        ploidy_summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
     output:
         vcf="{folder}/{sample}/snv_genotyping/{chrom,chr[0-9A-Z]+}.vcf",
     log:

diff --git a/workflow/rules/strandphaser.smk b/workflow/rules/strandphaser.smk
@@ -79,6 +79,7 @@ rule merge_strandphaser_vcfs:
     input:
         vcfs=aggregate_vcf_gz,
         tbis=aggregate_vcf_gz_tbi,
+        ploidy_summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
     output:
         vcfgz="{folder}/{sample}/strandphaser/phased-snvs/{sample}.vcf.gz",
     log: