bacass
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nf-core
Simple bacterial assembly and annotation pipeline
I got a "too many arguments" error for one of the commands when I had sample IDs with spaces in the sample sheet. I don't recall which command it was...
Hi, may I know is it possible to add [homopolish](https://github.com/ythuang0522/homopolish) as a tool for polishing after polished by medaka?
In the checks for long reads and fast5 files the wrong file is reported if there is an error https://github.com/nf-core/bacass/blob/959967364c7c0105b5b271acf0441fa9290e0d4c/subworkflows/local/input_check.nf#L66 Should read ``` exit 1, "ERROR: Please check input samplesheet...
Hi! I would like to know is there a way to set `default_jvm_mem_opts` in Pilon (which is a part of Unicycler) through `nextflow run` command line? Especially when one uses...
Hi, thank you for providing this pipeline. Would you consider providing [A5-miseq](https://anaconda.org/bioconda/a5-miseq) support for short-reads-only mode? I normally use Spades (or Unicycler in this case), but I've consistently been getting...
## PR checklist - [X] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add...
### Description of feature Many labs doing ONT sequencing generate basecalled/demultiplexed FASTQ output split into multiple files in the same directory (this is in fact the default behavior of MinKNOW...
### Description of the bug The pipeline usage documentation might need to be updated because there seems to be an issue in the nextflow run command when the `--assembly_type` parameter...
### Description of feature The` nf-validation` plugin will not receive any future updates. To ensure compatibility and receive future updates, please update your pipelines to use `nf-schema `instead. > Please...
### Description of feature I attempted to create a patch, but MultiQC version 1.21 does not properly parse the "file setup". It seems to require a deeper refactor as it...