Renato Alves
Renato Alves
### Which part of the project should be enhanced? User input or interface ### Is your enhancement request related to a problem? Please describe. In both CodiMD and HedgeDoc, adding...
Given the scenario: 1. Argument `--new` was renamed to `--old`. 2. `--old` should still do the same as `--new` but a warning should be printed. This use-case can be seen...
From the mailing list: ``` Hi all, since the latest NGLess release is v0.8.1 and the latest documented version v0.5.1 https://ngless.readthedocs.io/en/latest/releases.html https://ngless.readthedocs.io/en/latest/software.html as far as I can see, can anyone...
This can be seen when running for instance [the parallel test](https://github.com/ngless-toolkit/ngless/tree/master/tests/parallel) with `ngless --create-report -o report parallel.ngl`. The reason is that generating the final HTML report would require `collect()`ing reports...
When using `parallel`, I've occasionally run into a situation where all locks are marked as `.finished` but `collect()` still reports `Cannot collect (not all files present yet)`. In this case...
Currently NGLess uses two stages for execution. A first stage verifies that the script and output files are consistent (equivalent to `--validate-only`) and a second stage where computation happens if...
When working with very large SAM files it is often convenient to remove sequence and quality information to reduce storage and improve I/O. Following from this it would be convenient...
This was something that was requested in an offline discussion. Given a Fastq file with variable read length (e.g. after preprocessing): ``` mapped = select(mapped) using |mr|: mr = mr.filter(min_match_size={read_length},...
This error occurs when using `map()` together with `minimap2` and saving as a `.bam`. ``` import "minimap2" version "1.0" ... minimap_mapped = map(input, fafile=REFDB, mode_all=True, mapper="minimap2") write(minimap_mapped, ofile="output/" + sample...
This was noticed when setting up the [motus ngless-contrib module](https://github.com/ngless-toolkit/ngless-contrib/tree/master/motus.ngm). The following ngless script runs fine, but I'm not sure it should: ``` ngless "1.0" import "motus" version "2.1" ```...