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

@@ -208,16 +208,16 @@ inputBag:
       - inputBagOverride_PE_multiqc_data.json
     expire_in: 7 days
 
-  fastq:
-    stage: override
-    script:
-      - hostname
-      - ulimit -a
-      - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --fastqForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --ci true
-      - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
-      artifacts:
-        name: "$CI_JOB_NAME"
-        when: always
-        paths:
-          - fastqOverride_PE_multiqc_data.json
-        expire_in: 7 days
\ No newline at end of file
+fastq:
+  stage: override
+  script:
+  - hostname
+    - ulimit -a
+  - nextflow -q run ./workflow/rna-seq.nf --deriva ./test_data/auth/credential.json --bdbag ./test_data/auth/cookies.txt --repRID Q-Y5JA --fastqForce 'test_data/fastq/small/Q-Y5F6_1M.R{1,2}.fastq.gz' --ci true
+  - find . -type f -name "multiqc_data.json" -exec cp {} ./fastqOverride_PE_multiqc_data.json \;
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - fastqOverride_PE_multiqc_data.json
+    expire_in: 7 days
\ No newline at end of file