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snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

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config.yaml defaults

neavemj opened this issue · comments

commented

Good afternoon, thanks for the workflow!

In the default config.yaml on github, there is an example option like so:

config.yaml, line 37: star: "--outSAMtype BAM Unsorted"

However, if left in the config file it causes an error because then the STAR step gets two "--outSAMtype" flags. I realise defaults are meant to be changed, but I don't think this particular example can ever be used (because the flag is already hard-coded into the workflow).

Thanks again!

Matt.

commented

#41 will address this, so I'll try to follow up the problem there.