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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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hisat2-build expects fasta file, doe not accept fasta.gz - maybe warn earlier? #107

Closed smoe closed 2 years ago

smoe commented 2 years ago

Would you accept a patch to confirm at startup that all files are in the right format to avoid

Command: hisat2-build --wrapper basic-0 -f -p 2 /mariner/projects/HumanRabbitTFibrosisTimeSeries/genome/Homo_sapiens.GRCh38.dna.toplevel.fa.gz /mariner/projects/HumanRabbitTFibrosisTimeSeries/output/hisat2_index/GRCm38_index

That said, hisat2 should also see the same patch to bail out early.

borauyar commented 2 years ago

Yes, please :) Thank you!

borauyar commented 2 years ago

109 fixes this issue.