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nf-core / circdna

Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from cancer and other eukaryotic cells.
https://nf-co.re/circdna
MIT License
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No validation of --input_format #47

Closed lasseringstedmark closed 1 year ago

lasseringstedmark commented 1 year ago

Description of the bug

When using circdna with AmpliconArchitect for a already aligned BAM file, i ran into the following problem:

Access to 'SAMTOOLS_INDEX_BAM.out' is undefined since the process 'SAMTOOLS_INDEX_BAM' has not been invoked before accessing the output attribute

-- Check script '.nextflow/assets/nf-core/circdna/./workflows/circdna.nf' at line: 302 or see '.nextflow.log' file for more details

It seems that it is due to --input_format being without capital letters.

I think it would be nice it if either the --input_format is validated and clearly stated that this should be with capital letters or maybe simply ignore case.

By the way thanks for implementing the tool! :)

Command used and terminal output

No response

Relevant files

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System information

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DSchreyer commented 1 year ago

Hi, thanks for bringing this up to me. I added the parameter check and hope this solves some of the issues.

DSchreyer commented 1 year ago

I close this issue. It will be included in the newest udpate and is currently on the dev branch.