Comments (2)
Hi @winni2k!
We're currently not shipping the Salmon index with iGenomes (something we'd love to do but do not do at the moment). In the Salmon case, the lookup of the required genome files in iGenomes therefore fails. You should be able to get around this by supplying both the --fasta
and --gtf
parameters and not the --genome
one. Then the pipeline builds the indices on demand for you. You may later then reuse the salmon index built supplying it with --salmon_index ...
Let me know if that helps 👍
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This issue is likely fixed in the 2.1.0 release of the pipeline. If not, please open a new issue.
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Related Issues (20)
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