# Template for RNA-seq using Illumina prepared samples
# Michael Steinbaugh
#
# Homo sapiens
# YYYY-MM-DD
#
# Assuming a local run on a 16 core VM.
# bcbio_nextgen_py ../config/bcbio.yaml -t local -n 16
#
# Genome build is specific to the bcbio install.
# Run `bcbio_setup_genome.py` for list of genome builds.
#
# More template examples:
# https://github.com/bcbio/bcbio-nextgen/tree/master/config/templates
#
# Configuration documentation:
# https://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html
---
details:
  - analysis: RNA-seq
    genome_build: hg38
    algorithm:
      # Use HISAT2 instead of STAR for GRCh38/hg38.
      # STAR is recommended over HISAT2 for GRCh37/hg19.
      aligner: hisat2
      expression_caller: salmon

# Where to upload (save) the final output.
upload:
  dir: ../final

# Recommended run-specific resources.
resources:
  default:
    cores: 16
  tmp:
    dir: ~/scratch

# Template for RNA-seq using Illumina prepared samples
# Michael Steinbaugh
#
# Homo sapiens
# YYYY-MM-DD
#
# Assuming a local run on a 16 core VM.
# bcbio_nextgen_py ../config/bcbio.yaml -t local -n 16
#
# Genome build is specific to the bcbio install.
# Run `bcbio_setup_genome.py` for list of genome builds.
#
# More template examples:
# https://github.com/bcbio/bcbio-nextgen/tree/master/config/templates
#
# Configuration documentation:
# https://bcbio-nextgen.readthedocs.io/en/latest/contents/configuration.html
---
details:
  - analysis: RNA-seq
    genome_build: hg38
    algorithm:
      tools_on: [bcbiornaseq]
      # Use HISAT2 instead of STAR for GRCh38/hg38.
      # STAR is recommended over HISAT2 for GRCh37/hg19.
      aligner: hisat2
      expression_caller: salmon
      # This will automatically save a bcbioRNASeq S4 object for R.
      bcbiornaseq:
        organism: homo sapiens
        interesting_groups: [treatment, genotype]

# Where to upload (save) the final output.
upload:
  dir: ../final

# Recommended run-specific resources.
resources:
  default:
    cores: 16
  tmp:
    dir: ~/scratch

Enable bcbioRNASeq in the default template
Enable bcbioRNASeq in the default template
