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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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allow use of .gz when specifying fast and gtf #313

Open ChristopherMancuso opened 3 months ago

ChristopherMancuso commented 3 months ago

Description of feature

I was trying to run the scrnaseq pipeline specifying a fasta and gtf file. I downloaded from ensembl but they were gunzipped.

I searched Slack and found the same problem I was having and this answer that seems to have worked for me too https://nfcore.slack.com/archives/CHN5BV5DW/p1706103433405269

I was wondering if it would be possible to allow the use of .gz files like this? I have used the rnaseq pipeline and it allows for the use of gunzipped files. Thanks for this amazing resource!

grst commented 2 months ago

Will be fixed as part of #276.

nick-youngblut commented 2 months ago

Just for the gtf of refdata-gex-GRCh38-2024-A, the file size balloons from 61 Mb to 1.7 Gb when gunzip'd. It will be great to be able to use the gzip'd versions of the fasta and gtf files.

pinin4fjords commented 1 month ago

Still seems to be an issue in latest release

grst commented 1 month ago

276 has not been merged yet, this will be part of 2.7