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kevinrue / snakemake_alevin_10x

Snakemake pipeline for 10X using salmon alevin
MIT License
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Throw error if no input files are found for any sample #1

Closed kevinrue closed 4 years ago

kevinrue commented 4 years ago

If no files are glob'ed, the workflows generate commands without values for options -1 and -2, like this:

        salmon alevin -l ISR -i /ifs/mirror/alevin/salmon_partial_sa_index         -1  -2          -o results/pbmc_1k_v3 -p 16 --tgMap /ifs/mirror/alevin/txp2gene.tsv         --chromium --dumpFeatures          --expectCells 1000         2> logs/alevin/pbmc_1k_v3/rna.log