Jonathan Manning

Use default values

4

Thanks for the tool! Is there way to have it use default values from the schema where present, rather than faking values?

There is no way to assign multiple tags to one set of files in the asset directory

7

In my use I add a FASTA asset (a secondary one) like: ``` refgenie build homo_sapiens--GRCh38/fasta:cdna_ensembl95 --files fasta=Homo_sapiens.GRCh38.cdna.all.95.fa.gz ``` That works: ``` > refgenie list -g homo_sapiens--GRCh38 Local refgenie assets...

KeyError: 'aliases' - problem with concurrency?

5

Hi! Apologies in advance for the sketchy report, I'm having trouble pinning this down. I'm trying to build a large number of assets as part of a workflow. There's a...

Retain the effective `refgenie build` inputs

6

Hello! When we run analysis and present results to users, we report the reference files that were used, as provided by the reference resource (e.g. Ensembl). Switching to refgenie makes...

Ability to disable secondary behaviours for builds

1

Can I disable any of the post-processing the occurs with Refgenie build recipes? e.g. I have a GTF that seems to be failing in the bed conversion in ensembl_gtf due...

Specifying specific fasta tag in indexing

4

Hi! Thanks for refgenie- just getting my head around it and have a question. Using tags I seem to be able to create a reference genome and attach a cDNA...

Limitations of single config file

23

Hi! Just wanted to flag the limitations posed by a single config file. We have a use case where we may want to create 100s of assets at a time,...

Hi Nuno, I'd like to make a lightweight install-less version of iRAP available via Bioconda. It would just clone the repo and make the scripts and Makefiles available, allowing management...

Add shinyngs

1

Adds a recipe for my [shinyngs](https://github.com/pinin4fjords/shinyngs) R package which provides shiny applications for mining gene expression data. ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request...

Add gtf2featureannotation module

1

## PR checklist Adding module wrapper for https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. See also https://nfcore.slack.com/archives/CJRH30T6V/p1665413183508719. Apologies for the long name, didn't quite think that through at the time I wrote this tool! Closes https://github.com/nf-core/modules/issues/2316...