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Crash when specifying existing --star_index using star aligner #277
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Thanks for reporting! Would you like to submit a PR with the fix? |
Sure, currently doing a small test to make sure all works fine but looks ok... will see if I can do it later today! |
I'm still seeing this behaviour in 2.6.0 - did this fix not work? |
I met similar problem in 2.6.0. Setting --star_index with "/path/to/folder/" will end up with:
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I don't think anyone made the PR up to now. |
This is also a problem for all other aligners as far as I can tell. |
I applied the fix above, the star_index folder did not give any errors and STAR worked. But surprisingly, it only processed the first sample out of nine, even when it produced fastqc reports for all nine. Reverting this fix and letting the pipeline generate its own index made the pipeline work again as expected. Haven't had time to go through the code to find an explanation though. |
Good catch, it should be
The |
Jup, both the star_index and running multiple samples works now. Thanks for the quick and simple solution! |
should be fixed in dev, LMK if there are still issues. |
I'm still getting this error in 2.7.1 😦:
Only happens when I specify an existing star index. |
Description of the bug
When specifying an existing STAR index using the --star_index parameter the pipeline crashes and gives the following error:
This is because in this case the ch_star_index is defined as a file instead of a tuple which is expected by the starsolo subworkflow (and which is also returned by STAR_GENOMEGENERATE in case no existing star genome is specified).
scrnaseq.nf:
This can be fixed by adjust the line above to:
Command used and terminal output
Output:
The text was updated successfully, but these errors were encountered: