Gregor Sturm

Packing fails with FileNotFoundError despite `--ignore-missing-files`

2

I am trying to pack an environment with the following command: ``` conda-pack -n pircher-sc-integrate2 -o /local/scratch/sturm/285d084a09d61ed4468ebc71a1444339//packed_environment.tar.gz --ignore-missing-files --force ``` It fails with the following error message ```pytb Packing environment...

embed_file is limited to 2MB file size in Chrome

9

I used `xfun::embed_file` with a several MB large file. While the link works perfectly in Firefox, I get a `Network error` when trying to download the same file in Chrome....

Switch from alevin to alevin-fry

20

## Is your feature request related to a problem? Please describe `alevin-fry` is the successor of `alevin` and this pipeline should use the latest-greatest version! @rob-p pointed out on slack...

Improve QC reports

5

## Is your feature request related to a problem? Please describe I find quality control reports per sample (number of detected cells, number of genes per cell etc.) very useful...

Default genomes and genome annotation

1

The pipeline should bet set-up to run with default genomes and genome annotations (iGenomes?). Where possible, also pre-built indexes should be used. This feature was temporarily removed in #76 and...

Call empty droplets

1

## Is your feature request related to a problem? Please describe I think it could be nice to have a step to distinguish empty droplets from actual cells. As far...

Alevin workflow cannot handle gzipped genomes or gtf files

1

Tested on DSL2 version in dev. Either update modules to handle gzip files, or include an optional gunzip process.

Add TRUST4 for VDJ calling

1

## Is your feature request related to a problem? Please describe TRUST4 claims they can call TCRs not only from VDJ-enriched 10x data, but also regular 10x 5' seq and...

Pytest workflow makes it easier to maintain larger test suites and also allows to check outputs. cf. https://github.com/nf-core/tools/issues/605, https://github.com/nf-core/rnaseq/pull/546, https://github.com/nf-core/sarek/tree/dev/tests Testing scenarios: * Run pipeline with more than one file...

Detect and remove cell-free mRNA contamination

2

## Is your feature request related to a problem? Please describe I think it would be good to have [SoupX](https://github.com/constantAmateur/SoupX) or a similar tool as part of the pipeline. ##...