Simon Heumos

MultiQC's ODGI module - How to bring all ASCII character counts of a graph into a table?

3

### Description of feature Hi there @ewels :) When working with variation graphs, the sequences in the nodes can be nucleotides, amino acids, RNA sequences, etc. In the end what...

MultiQC v1.12 ignores config file given via `-c`

5

### Description of bug MultiQC v1.12 ignores the config file I add via the command line. ### File that triggers the error https://fex.belwue.de/fop/ug3PCHXy/Mambo3.tar All files are reachable via this link...

binding VG on linux

6

Hi, I have trouble binding the `vg` lib on linux. Somehow the linking does not work and I don't know why. If I add a wrong library path, then the...

comparison of default values returns unclear error

2

### Description of the bug Just run `nf-core schema build` to edit some arguments. However, some arguments were flagged as not matching, although they looked perfectly identical! The underlying issue...

Completely turn off new clipping behaviour

4

Hi @maickrau Since the new release and as you mentioned in https://github.com/maickrau/GraphAligner/issues/28, per default `--precise-clipping` is turned on. For my evaluation of reconstruction accuracy, I would like to turn this...

GraphAligner is not deterministic - Is this fixable

4

Hi @maickrau it seems that GraphAligner is non-deterministic. Small example: ``` GraphAligner -g cerevisiae.pan.fa.pggb-W-s50000-p90-n5-a0-K16-k8.seqwish-w30000-j5000-e5000-I0.7.smooth.consensus@10\:y.gfa -f cerevisiae.pan.fa -a cerevisiae.pan.fa.pggb-W-s50000-p90-n5-a0-K16-k8.seqwish-w30000-j5000-e5000-I0.7.smooth.consensus@10\:y.gfa_RUN1.gaf -t 16 -x vg GraphAligner -g cerevisiae.pan.fa.pggb-W-s50000-p90-n5-a0-K16-k8.seqwish-w30000-j5000-e5000-I0.7.smooth.consensus@10\:y.gfa -f cerevisiae.pan.fa -a cerevisiae.pan.fa.pggb-W-s50000-p90-n5-a0-K16-k8.seqwish-w30000-j5000-e5000-I0.7.smooth.consensus@10\:y.gfa_RUN2.gaf -t...

Hi @chfi, I wanted to use your `gafpaf.rs` in order to improve the code in https://github.com/subwaystation/rs-peanut. However, you don't store the `id:f:` field. Are there any objections to change that?...

Scaling Issue of Drawn Bases when Zooming.

5

Hi There :) When I zoom (in or out), the scaling of the drawn bases usually does not fit anymore. They are drawn too wide. Best, Simon

handle reversing self edges in divide_handle in odgi

1

This should fix https://github.com/vgteam/vg/issues/3020.

Use `grabix` to detect compression mode of FASTA input.

2

## Is your feature request related to a problem? Please describe If I enter give `nf-core/pangenome` a GZIP compressed FASTA as input, `WFMASH` will complain. ## Describe the solution you'd...