CHANGELOG.md



To find the state of this project's repository at the time of any of these versions, check out the tags.


v0.0.4 (in development)
User Facing
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Background
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Known Bugs

outputBag does not contain fetch for processed data
Does not include automatic data upload
Override params (inputBag, fastq, species) aren't checked for integrity


v0.0.3
User Facing

TPM table:

Add Ensembl Gene ID
Rename columns: GENCODE_Gene_Symbol, Ensembl_GeneID, NCBI_GeneID


MultiQC output custom tables (html+JSON):

Run table: Session ID and Pipeline Version

Reference Table: Species, Genome Reference Consortium Build, Genome Reference Consortium Patch, GENCODE Annotation Release (outputs both human and mouse versions)


Add inputBag override param (inputBagForce) [*.zip]

Uses provided inputBag instead of downloading from data-hub
Still requires matching repRID input param


Add fastq override param (fastqsForce) [R1,R2]

Uses provided fastq instead of downloading from data-hub
Still requires matching repRID input param and will pull inputBag from data-hub to access submitted metadata for reporting


Add species override param (speciesForce) [Mus musculus or Homo sapiens]

forces the use of the provided species
ignores inferred ambiguous species


Background