documentation: salmon quant is run when skip_pseudo_alignment: True if strandedness set auto

[savagjh]

Description of the bug

I received

20:20:40.401] [jointLog] [warning] salmon was only able to assign 0 fragments to transcripts in the index, but the minimum number of required assigned fragments (--minAssignedFrags) was 10. This could be indicative of a mismatch between the reference and sample, or a very bad sample.  You can change the --minAssignedFrags parameter to force salmon to quantify with fewer assigned fragments (must have at least 1).

And so tried setting skip_pseudo_alignment: True. I did not realize that setting strandedness to auto caused SALMON_QUANT in the FASTQ_SUBSAMPLE_FQ_SALMON subworkflow to run (per @maxulysse ).

Command used and terminal output

Relevant files

No response

System information

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