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nf-core / fastquorum

Pipeline to produce consensus reads using unique molecular indexes/barcodes (UMIs)
https://nf-co.re/fastquorum
MIT License
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Fix passing filter_min_reads as int #62

Closed prot-devin closed 3 months ago

prot-devin commented 3 months ago

Description of the bug

When analyzing non-duplex reads it makes sense to set filter_min_reads to an int, however. when setting --filter_min_reads 1 you will encounter the following error: --filter_min_reads: expected type: String, found: Integer (1)

even passing --filter_min_reads "1" does not seem to solve this issue.

Command used and terminal output

nextflow run nf-core/fastquorum --input $sample_sheet --outdir $outdir --fasta $reference_fasta --mode rd --groupreadsbyumi_strategy Identity --groupreadsbyumi_edits 0 --duplex_seq false --filter_min_reads 1 -profile docker -resume

Error message: 
--filter_min_reads: expected type: String, found: Integer (1)

Relevant files

No response

System information

Nextflow version: 24.04.2 Hardware: HPC Executor: slurm Container: docker/singularity OS: Ubuntu nf-core/fastquorum v1.0.1dev

prot-devin commented 3 months ago

@SPPearce has suggested a workaround of --filter_min_reads '"1"' for the time being

SPPearce commented 3 months ago

Fixed in #66