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

test_data/createTestData.sh

@@ -9,12 +9,12 @@ mkdir -p NEW_test_data
 
 ln -sfn `readlink -e ./test_data/auth/credential.json` ~/.deriva/credential.json
 
-mkdir -p ./NEW_test_data/bagit
+mkdir -p ./NEW_test_data/bag
 singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' deriva-download-cli dev.gudmap.org --catalog 2 ./workflow/conf/replicate_export_config.json . rid=Q-Y5F6
-cp Replicate_Q-Y5F6.zip ./NEW_test_data/bagit/Replicate_Q-Y5F6.zip
+cp Replicate_Q-Y5F6.zip ./NEW_test_data/bag/Replicate_Q-Y5F6.zip
 
 mkdir -p ./NEW_test_data/fastq
-unzip ./test_data/bagit/Replicate_Q-Y5F6.zip
+unzip ./test_data/bag/Replicate_Q-Y5F6.zip
 singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' bash ./workflow/scripts/bdbagFetch.sh Replicate_Q-Y5F6 Replicate_Q-Y5F6
 cp Replicate_Q-Y5F6.R1.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R1.fastq.gz
 cp Replicate_Q-Y5F6.R2.fastq.gz ./NEW_test_data/fastq/Replicate_Q-Y5F6.R2.fastq.gz