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icgc-argo / seq-tools

Command line tools for ARGO sequencing data validation
https://github.com/icgc-argo/seq-tools
GNU Affero General Public License v3.0
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C691 update2 #105

Open edsu7 opened 1 year ago

edsu7 commented 1 year ago

Added the following tests to check for strandedness in RNA-seq fasta:

tests/submissions/SRR5196915.invalid/SRR5196915.json
tests/submissions/SRR5196915.valid.with-skip-strand-and-skip-md5/SRR5196915.RNAseq.fastq.valid.json
tests/submissions/SRR5196915.valid.with-skip-strand/SRR5196915.RNAseq.fastq.valid.json
tests/submissions/SRR5196915/SRR5196915.json

Additionally will check for local salmon installation, erroring out not found and library is RNA-seq.

Added skip for RNA-seq related tests in test_validations.py