upload:
  dir: upload
fc_date: '110907'
fc_name: ERP000591
details:
  - analysis: RNA-seq
    algorithm:
      rsem: True
      aligner: tophat2
      trim_reads: read_through
      adapters: [truseq, polya]
      assemble_transcripts: True
    description: Test1
    files:
      - ../data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt
      - ../data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt
    #files: ["s3://bcbio_nextgen/testing/1_110907_ERP000591_1_fastq.txt.gz", "s3://bcbio_nextgen/testing/1_110907_ERP000591_2_fastq.txt.gz"]
    genome_build: mm9
    lane: 1

upload:
  dir: upload
fc_date: '110907'
fc_name: ERP000591
details:
  - analysis: RNA-seq
    algorithm:
      transcriptome_align: True
      aligner: tophat2
      trim_reads: read_through
      adapters: [truseq, polya]
      assemble_transcripts: True
    description: Test1
    files:
      - ../data/110907_ERP000591/1_110907_ERP000591_1_fastq.txt
      - ../data/110907_ERP000591/1_110907_ERP000591_2_fastq.txt
    #files: ["s3://bcbio_nextgen/testing/1_110907_ERP000591_1_fastq.txt.gz", "s3://bcbio_nextgen/testing/1_110907_ERP000591_2_fastq.txt.gz"]
    genome_build: mm9
    lane: 1

Change rsem to transcriptome_align in all of the test config files.
Change rsem to transcriptome_align in all of the test config files.
