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Gervaise Henry authoredf7559c64
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CHANGELOG.md 5.89 KiB
v1.0.3 (in development)
User Facing
Background
- Add memory limit per thread for samtools sort (#108)
- Remove parsing restrictions for submitted stranded/spike/species (#105, #106)
- Pass unidentified ends instead of overwriting it as unknown
- Move fastqc process before trim to catch fastq errors (#107)
- Only use fastq's that match *[_.]R[1-2].fastq.gz naming convention (#107)
- Add error output for no fastq's
- Update input bag export config to only fetch fastq's that match *[_.]R[1-2].fastq.gz naming convention
- Remove check for multiple fastq check in parse metadata (redundant and no longer valid)
- Handle blank submitted endness better
- Don't use file.csv from inputBag to parse manual endness, use counted from getData
- Detect malformed fastq's (#107)
Known Bugs
- Override params (inputBag, fastq, species) aren't checked for integrity
- Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included)
v1.0.2
User Facing
Background
- Fix spelling in config file for process of failed fastq to upload error message (#104)
Known Bugs
- Override params (inputBag, fastq, species) aren't checked for integrity
- Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included)
v1.0.1
User Facing
Background
- Split non-metadata mismatch error handling proces into 2, 1 to handle fastq errors and one for species errors (BUG FIX #101)
- Add known errors to integration CI tests (ambiguous species, trunkated fastq, R1/R2 mismatch (#103)
- Fix pre exeuction run fails uploading of execution run RID to tracking site (#96, #97)
- Change CI replicate count badge CI to count all execution runs that match major version
Known Bugs
- Override params (inputBag, fastq, species) aren't checked for integrity
- Authentication files and tokens must be active (active auth client) for the duration of the pipeline run (until long-lived token utilization included)