diff --git a/CHANGELOG.md b/CHANGELOG.md index e4072e3811212264381480e34d5bebb96ecb3454..496ad6759720ecc5b5ee1adde62528ddb75b0c85 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,13 @@ # v0.0.4 (in development) **User Facing** -* +* Add option to pull references from datahub **Background** -* +* Remove (comment out) option to pull references from S3 +* Make pull references from BioHPC default (including in biohpc.config) *Known Bugs* +* Datahub reference pull uses dev.gudmap.org as source until referencencs are placed on production * outputBag does not contain fetch for processed data * Does not include automatic data upload * Override params (inputBag, fastq, species) aren't checked for integrity diff --git a/README.md b/README.md index 49069c53ada7b1f8351684cea8ba161830369208..e3134bf4b3b6d7cbe0521fe58d7567ec44f34da4 100644 --- a/README.md +++ b/README.md @@ -49,6 +49,9 @@ To Run: * *current mouse* **38.p6.vM22** = GRCm38.p6 with GENCODE annotation release M22 * *current human* **38.p6.v31** = GRCh38.p12 with GENCODE annotation release 31 * ***Optional*** input overrides + * `--refSource` source for pulling references + * **biohpc** = source references from BICF_Core gudmap reference local location (workflow must be run on BioHPC system) + * **datahub** = source references from GUDMAP/RBK reference_table location (currently uses dev.gudmap.org) * `--inputBagForce` utilizes a local replicate inputBag instead of downloading from the data-hub (still requires accurate repRID input) * eg: `--inputBagForce test_data/bag/Replicate_Q-Y5F6.zip` (must be the expected bag structure) * `--fastqsForce` utilizes local fastq's instead of downloading from the data-hub (still requires accurate repRID input)