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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. |
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: