SchwarzMarek

Hi, I'm playing a little with bowtie2 scoring (for more flexibility) and I've noticed that if I multiply all scoring parameters by a factor of 10, I get slightly different...

### Description of the bug The `--skip_fastq_download` flag implies that only the `fastq` files will not be downloaded. When using the `--skip_fastq_download` and `--nf_core_pipeline rnaseq` together, the `fastq` files are...

Annotation format and column meaning

1

Hello, thanks for the pipeline I' want to use different reference and needed to convert annotations as suggested in documentation. To get the feel about the annotation format, I've looked...

https://github.com/OpenGene/fastp/blob/7a2ba61ece247695eeefae289b4b813b821a947e/src/main.cpp#L322

kmerfinder update and optimization

1

### Description of feature I very much appreciate the functionality implemented with kmerfinder (that is automatic search for close genome and running Quast with it). However I'm running into several...

### Description of the bug Nanopolish doesn't run due to invalid input to MINIMAP2_POLISH step. ### Command used and terminal output ```consolenextflow run nf-core/bacass --input bso.tsv -profile docker --skip_kraken2 --assembler...