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

.gitlab-ci.yml

@@ -231,10 +231,10 @@ integration_se:
       - output/report/
       - SE_multiqc_data.json
     expire_in: 7 days
-    retry:
-      max: 1
-      when:
-        - always
+  retry:
+    max: 1
+    when:
+      - always
 
 integration_pe:
   stage: integration
@@ -257,17 +257,18 @@ integration_pe:
       - output/report/
       - PE_multiqc_data.json
     expire_in: 7 days
-    retry:
-      max: 1
-      when:
-        - always
+  retry:
+    max: 1
+    when:
+      - always
 
 override_inputBag:
   stage: integration
   only:
     - merge_requests
+  except:
     refs:
-      - develop
+      - master
   script:
   - hostname
   - ulimit -a
@@ -279,17 +280,18 @@ override_inputBag:
     paths:
       - inputBagOverride_PE_multiqc_data.json
     expire_in: 7 days
-    retry:
-      max: 1
-      when:
-        - always
+  retry:
+    max: 1
+    when:
+      - always
 
 override_fastq:
   stage: integration
   only:
     - merge_requests
+  except:
     refs:
-      - develop
+      - master
   script:
   - hostname
   - ulimit -a
@@ -301,16 +303,15 @@ override_fastq:
     paths:
       - fastqOverride_PE_multiqc_data.json
     expire_in: 7 days
-    retry:
-      max: 1
-      when:
-        - always
+  retry:
+    max: 1
+    when:
+      - always
     
 override_species:
   stage: integration
   only:
     - merge_requests
-    - tags
   except:
     refs:
       - master
@@ -325,10 +326,10 @@ override_species:
     paths:
       - speciesOverride_PE_multiqc_data.json
     expire_in: 7 days
-    retry:
-      max: 1
-      when:
-        - always
+  retry:
+    max: 1
+    when:
+      - always
   
 
 consistency: