may need to modify the rule mark_ duplicates

[user-tq]

When trying to allow this pipeline, I encountered an error

 bams = snakemake.input.bams
           ^^^^^^^^^^^^^^^^^^^^
AttributeError: 'InputFiles' object has no attribute 'bams'

Due to network reasons, localized wrapper and varlocaliraptor and forced varlocaliraptor to use version 1.23.5 wrapper, which made it relatively easy for me to find the problem.（Or maybe this is a problem created by me. Sorry, I'm not an expert in this field）

I insert in the picard/markduplicates/wrapper.py

print(snakemake.__dict__)
print(snakemake.input.__dict__)

i think is wrong to write

rule mark_duplicates:
    input:
        lambda wc: "results/mapped/{sample}.bam"
        if units.loc[wc.sample, "umis"].isnull().any()
        else "results/mapped/{sample}.annotated.bam",

maybe it should be

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

[dlaehnemann]

Yes, you are right that the wrapper changed and the workflow here doesn't reflect that change in the input specification. Would you feel comfortable submitting a pull request with your suggested change (which should indeed fix this)?

[dlaehnemann]

Closed by #217 .