fix: update mark_duplicates to newest wrapper syntax (#217)

* Update mapping.smk

* fix mark_duplicates according to the new wrapper

* amend the Formatting failure according to: https://github.com/github/super-linter/issues/1397#issuecomment-805249812

---------

Co-authored-by: David Laehnemann <david.laehnemann@hhu.de>

.github/workflows/main.yml

@@ -12,6 +12,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
+        with:
+          # Full git history is needed to get a proper
+          # list of changed files within `super-linter`
+          fetch-depth: 0
       - name: Formatting
         uses: github/super-linter@v4
         env:

workflow/rules/mapping.smk

@@ -31,7 +31,7 @@ rule annotate_umis:
 
 rule mark_duplicates:
     input:
-        lambda wc: "results/mapped/{sample}.bam"
+        bams=lambda wc: "results/mapped/{sample}.bam"
         if units.loc[wc.sample, "umis"].isnull().any()
         else "results/mapped/{sample}.annotated.bam",
     output: