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snakemake-workflows / dna-seq-varlociraptor

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
MIT License
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issues with cutadapt #155

Open piecrivello opened 1 year ago

piecrivello commented 1 year ago

Hi everyone,

I am having trouble using this pipeline apparently at the step of cutadapt.

For my analysis I submitted already trimmed fastq files, and so I left empty the adapters field in units.tsv and I deactivated trimming in the config.yaml.

By running the pipeline, I got errors from the rules cutadapt-pe and cutadapt-pipe with no information in their corresponding log files. The only informative massage seems to be in the terminal as the following:

Traceback (most recent call last):
  File "/mnt/data/crivellopi/Bioinformatics/dna-seq-varlociraptor/.snakemake/scripts/tmpgsy5av3k.wrapper.py", line 23, in <module>
    assert (
AssertionError: No options provided to cutadapt. Please use 'params: adapters=' or 'params: extra='.

I hope you can help me solving this.

All the best, Pietro

Austin-s-h commented 1 year ago

https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/pull/67 Should also be applicable wherever cutadapt is used