/*
 * -------------------------------------------------
 *  Nextflow config file for running tests
 * -------------------------------------------------
 * Defines bundled input files and everything required
 * to run a fast and simple test. Use as follows:
 *   nextflow run nf-core/rnaseq -profile test,<docker/singularity>
 */

params {
  config_profile_name        = 'Test profile'
  config_profile_description = 'Minimal test dataset to check pipeline function'

  // Limit resources so that this can run CI
  max_cpus   = 2
  max_memory = 6.GB
  max_time   = 48.h

  // Input data
  input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/samplesheet.csv'

  // Genome references
  fasta            = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
  gtf              = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz'
  gff              = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz'
  transcript_fasta = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta'
  additional_fasta = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz'

  hisat2_index     = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz'
  star_index       = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz'
  salmon_index     = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz'
  rsem_index       = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz'

  // Other parameters
  pseudo_aligner      = 'salmon'
  umitools_bc_pattern = 'NNNN'

  // When using RSEM, remove warning from STAR whilst building tiny indices
  modules {
    'rsem_preparereference' {
      args2 = "--genomeSAindexNbases 7"
    }
  }
}


