cluster:
  name: odyssey
  profile: lsf
  cores: 1

log_dir: log

dir:
  results: results/test/tophat1
  data: data
  meta: meta
  tmp: tmp

gtf: test/data/E_coli_k12.ASM584v1.15.gtf
ref: test/data/bowtie/e_coli

program:
  tophat: tophat
  bowtie: bowtie

input:
  - [test/data/s_1_1_10k.fq, test/data/s_1_2_10k.fq]
  - [test/data/s_1_1_10k_last.fq]

stage:
  tophat:
    name: tophat
    program: tophat
    quality_format: None
    max_errors: 2

run:
  [tophat]

cluster:
  name: odyssey
  profile: lsf
  cores: 1

log_dir: log

dir:
  results: results/test/tophat1
  data: data
  meta: meta
  tmp: tmp

gtf: test/data/E_coli_k12.ASM584v1.15.gtf
ref: test/data/bowtie/e_coli

program:
  tophat: tophat
  bowtie: bowtie

input:
  - [test/data/s_1_1_10k.fq, test/data/s_1_2_10k.fq]
  - [test/data/s_1_1_10k_last.fq]

stage:
  tophat:
    name: tophat
    program: tophat
    quality_format: illumina
    max_errors: 2

run:
  [tophat]

Use illumina file format for testing.
Use illumina file format for testing.
