fix: config keys for test diles, formatting

snakemake-workflows · Sep 30, 2024 · dd057c7 · dd057c7
1 parent ff5c44e
commit dd057c7
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Showing 2 changed files with 9 additions and 5 deletions.
diff --git a/.test/config-simple/config.yml b/.test/config-simple/config.yml
@@ -39,10 +39,10 @@ maximum_secondary: 100
 secondary_score_ratio: 1.0
 
 # Samtools view opts, "-b" creates BAM from SAM.
-sview_opts: "-b"
+samtobam_opts: "-b"
 
 # Samtools sort opts,
-ssort_opts: ""
+bamsort_opts: ""
 
 # Salmon library type
 salmon_libtype: "U"
@@ -51,7 +51,7 @@ salmon_libtype: "U"
 # QC options
 
 # Samtools stats opts
-sstats_opts: ""
+bamstats_opts: ""
 
 # Count filtering options - customize these according to your experimental design:
 

diff --git a/workflow/rules/commons.smk b/workflow/rules/commons.smk
@@ -65,10 +65,14 @@ def aggregate_input(samples):
 def rule_all_input():
     all_input = list()
     all_input.append("versions.txt")
-    all_input.extend(expand("NanoPlot/{sample}/NanoPlot-report.html", sample=samples["sample"]))
+    all_input.extend(
+        expand("NanoPlot/{sample}/NanoPlot-report.html", sample=samples["sample"])
+    )
     all_input.append("NanoPlot/all_samples/NanoPlot-report.html")
     all_input.extend(expand("QC/samstats/{sample}.txt", sample=samples["sample"]))
-    all_input.extend(expand("qualimap/{sample}/qualimapReport.html", sample=samples["sample"]))
+    all_input.extend(
+        expand("qualimap/{sample}/qualimapReport.html", sample=samples["sample"])
+    )
     all_input.extend(
         expand("counts/{sample}_salmon/quant.sf", sample=samples["sample"])
     )