diff --git a/CHANGELOG.md b/CHANGELOG.md index b6dae18ebf4507589d204b5d8d6e3e6ff3893c32..532a227128ea5d1d384384af06c68efce165cec6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,12 @@ * Update references to use bags * Update to newer references (GRCh38.p13.v36 and GRCm38.p6.vM25) * Use production server for data-hub reference call -* Stop pipeline if submitted does not match infered +* Error pipeline if submitted does not match infered * Update execution run with "Success" or "Error" +* Error if fastq error (>2, if pe != 2, if se !=1) +* Error if pe and line count of R1 != R2 +* Error if ambiguous species inference +* Remove non fastq from inputBag from the export bag config level **Background** * Remove (comment out) option to pull references from S3 @@ -23,12 +27,12 @@ * Change docker images to production * Add automated version badges * Only calculate/report tin values on regular chromosomes (from gtf) -* **NEED TO UPDATE getRef for CI unit** +* Change inputBag fetch to manifest then validate (if fail fetch missing and revalidate up to 3 times) +* Retry getData and trimData processes up to once *Known Bugs* * Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production * Override params (inputBag, fastq, species) aren't checked for integrity -* <hr>