maca_chr19_samplesheet.conf

/*
 * -------------------------------------------------
 *  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/sicilian -profile test,<docker/singularity>
 */

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

  max_cpus = 2
  // max_memory = 6.GB
  max_time = 48.h
  outdir = './results'
  // Input data
  // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
  // TODO nf-core: Give any required params for the test so that command line flags are not needed
  single_end = false
  input = false
  skip_umitools = false
  input_csv = 'maca_bladder_samplesheet.csv'
  star_index = 's3://salzman-lab/nf-sicilian-outputs/aws-maca-small-chr19/genome/index/star/'
  fasta = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/mm10_chrom19.fa'
  gtf = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/GCF_000001635.26_GRCm38.p6_genomic.chr19.gtf.gz'
  // sicilian_class_input_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['glm_subscript_out_of_bounds/MACA_24m_M_BLADDER_58__class_input.tsv']],
  //   ['MACA_24m_M_BLADDER_59', ['glm_subscript_out_of_bounds/MACA_24m_M_BLADDER_59__class_input.tsv']],
  // ]
  // star_bam_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['s3://salzman-lab/nf-sicilian-outputs/aws-maca-small-chr19/star/MACA_24m_M_BLADDER_58.Aligned.out.bam']],
  //   ['MACA_24m_M_BLADDER_59', ['s3://salzman-lab/nf-sicilian-outputs/aws-maca-small-chr19/star/MACA_24m_M_BLADDER_59.Aligned.out.bam']],
  // ]
  // star_sj_out_tab_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['glm_subscript_out_of_bounds/MACA_24m_M_BLADDER_58.SJ.out.tab']],
  // ]
  // star_reads_per_gene_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['glm_subscript_out_of_bounds/MACA_24m_M_BLADDER_58.ReadsPerGene.out.tab']],
  // ]
  // star_chimeric_junction_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['glm_subscript_out_of_bounds/MACA_24m_M_BLADDER_58.Chimeric.out.junction']],
  // ]
  // sicilian_glm_output_paths = [
  //   ['MACA_24m_M_BLADDER_58', ['s3://salzman-lab/nf-sicilian-outputs/aws-maca-small-chr19/sicilian/glm/MACA_24m_M_BLADDER_58__GLM_output.txt']],
  // ]
  domain = 's3://salzman-lab/hg38_ref_files/domain_file.txt'
  save_reference = true
  stranded = true
  tenx = true
  annotator = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_gene_names.pkl'
  exon_bounds = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_exon_bounds.pkl'
  splices = 'https://github.com/czbiohub/test-datasets/raw/olgabot/sicilian/reference/sicilian/GCF_000001635_splices.pkl'
  // Ignore `--input` as otherwise the parameter validation will throw an error
  schema_ignore_params = 'genomes,input_paths,input'


}

process {
  executor = 'awsbatch'
  queue = 'default-971039e0-830c-11e9-9e0b-02c5b84a8036'
  errorStrategy = { task.exitStatus in [143,137,104,134,139,160] ? 'retry' : 'finish' }
  maxRetries = 1
}

tower {
  endpoint = 'http://nftower.czbiohub.org:8000/api'
  enabled = true
}