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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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reference_build parameter doesn't accept 'mm10' as input #42

Closed ipstone closed 1 year ago

ipstone commented 1 year ago

Description of the bug

Running the following command:

nextflow run nf-core/circdna -r 1.0.1 --input samplesheet_bam.csv --outdir ./output --genome mm10 -profile singularity --circle_identifier ampliconarchitect --aa_data_repo ./aa_data_repo --fasta ... --mosek_license_dir ~/.config/mosek --reference_build mm10

will generate the error:

Reference Build not given! Please specify --reference_build 'hg19', 'GRCh38', or 'GRCh37'.

The code checking this condition is at: https://github.com/nf-core/circdna/blob/8ff55299f17693fe25b5221b1c0d93ac08c06b14/workflows/circdna.nf#L51

This condition probably needs to be updated to allow the pipeline to run on mm10 mouse samples.

Thanks

Command used and terminal output

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Relevant files

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System information

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DSchreyer commented 1 year ago

Thanks for bringing this up to me. The AmpliconArchitect branch is not yet updated for mm10, yet. I think it should be easy to do and hope I can do it over the holidays.

DSchreyer commented 1 year ago

Hi, I pushed the changes on to dev. Would you be willing to pull dev and check if this solved the issue?

ipstone commented 1 year ago

Thanks @DSchreyer - I tried the dev branch, it solves the issue, thanks!