Siebren Frölich
Siebren Frölich
Since the rule is trackhub_index, I guess that any genes on that contig are unsearchable on UCSC. So perhaps its fine to ignore the error then...
``` -allErrors - skip groups with errors rather than aborting. Useful for getting infomation about as many errors as possible. ``` **I think** it means it just skips the lines...
Spur_5.0 has different contig names in the genome fasta and the annotation. NCBI will have to fix this, or you must manually change them :(
`deseq2science` currently needs to parse the samples.tsv file within R, so we'll still need this function anyway. Can let this go stale... We could refactor deseq2science, and make it a...
wrong button
Snakefmt improves readability a bit, but still needs supervision. Lets keep this open for now, and I'll make a PR manually this time.
we already use the package for strandedness! I'll have a look next time I'm in a programming mood ;)
A config flag to (not) remove the conda environments on a successful run sounds like it could be useful. It should also be clear enough for anyone who takes the...
> @siebrenf I remember we had some file-latency ish error in the past with genomepy. The rule was registred as finished succesfully, but it was still running in the background...
If the ATAC-seq run did work, but you get timeouts and unexplained errors, then maybe the issue is the server occupancy/load? This is a longshot, but you could try to...