0.0.3

• 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
• Add GeneSymbol/EnsemblID/EntrezID translation files to references

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated
• Replace dag.png with the most recent CI pipleine integrated_pe artifact
• CHANGELOG.md is updated
• README.md is updated
• LICENSE.md is updated with new contributors
• Docker images moved to production release and changed in pipeline
• Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #61 (closed) Closes #71 (closed) Closes #72 (closed) Closes #73 (closed) Closes #74 (closed)

/cc @ghenry @venkat.malladi

CHANGELOG.md

@@ -3,9 +3,9 @@
 * TPM table:
   * Add Ensembl Gene ID
   * Rename columns: *GENCODE_Gene_Symbol*, *Ensembl_GeneID*, *NCBI_GeneID*
-* MultiQC output custom talbes (html+JSON):
+* 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* (ouputs both human and mouse versions)
+  * 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
@@ -14,7 +14,7 @@
   * 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
-  * ignors infered ambiguous species
+  * ignores inferred ambiguous species
 
 **Background**
 * Add GeneSymbol/EnsemblID/EntrezID translation files to references
@@ -22,7 +22,7 @@
 *Known Bugs*
 * outputBag does not contain fetch for processed data
 * Does not include automatic data upload
-* Override params (inputBag, fastq, species) are't checked for integrity
+* Override params (inputBag, fastq, species) aren't checked for integrity
 
 <hr>
 
@@ -47,4 +47,4 @@
 **INITIAL BETA VERSION**\
 Does not include automatic data upload\
 This version is for initial upload of test data to GUDMAP/RBK data-hub for internal integration
-<hr>
+<hr>
\ No newline at end of file