Updating GH actions, small fixes for v8 upgrade

friendsofstrandseq · Jun 20, 2024 · 7e8ac18 · 7e8ac18
1 parent 9e32b48
commit 7e8ac18
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Showing 2 changed files with 7 additions and 9 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -908,13 +908,13 @@ def get_all_plots(wildcards):
 
         # Run summary section
 
-        # l_outputs.extend(
-        #     expand(
-        #         "{folder}/{sample}/config/run_summary.txt",
-        #         folder=config["data_location"],
-        #         sample=wildcards.sample,
-        #     ),
-        # )
+        l_outputs.extend(
+            expand(
+                "{folder}/{sample}/config/run_summary.txt",
+                folder=config["data_location"],
+                sample=wildcards.sample,
+            ),
+        )
 
     # from pprint import pprint
     # pprint(l_outputs)

diff --git a/workflow/rules/strandphaser.smk b/workflow/rules/strandphaser.smk
@@ -48,7 +48,6 @@ rule run_strandphaser_per_chrom:
         bsgenome="workflow/data/ref_genomes/config/BSgenome_{}.ok".format(
             config["reference"]
         ),
-        summary="{folder}/{sample}/ploidy/ploidy_summary.txt",
     output:
         "{folder}/{sample}/strandphaser/StrandPhaseR_analysis.{chrom}/Phased/phased_haps.txt",
         "{folder}/{sample}/strandphaser/StrandPhaseR_analysis.{chrom}/VCFfiles/{chrom}_phased.vcf",
@@ -76,7 +75,6 @@ rule run_strandphaser_per_chrom:
         """
 
 
-ruleorder: summarise_ploidy > merge_strandphaser_vcfs
 
 
 rule merge_strandphaser_vcfs: