environment.yml

# You can use this file to create a conda environment for this pipeline:
#   conda env create -f environment.yml
name: nf-core-rnaseq-1.4.2
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  ## conda-forge packages, sorting now alphabetically, without the channel prefix!
  - matplotlib=3.0.3        # Current 3.1.0 build incompatible with multiqc=1.7
  - r-base=3.6.1
  - conda-forge::r-data.table=1.12.4
  - conda-forge::r-gplots=3.0.1.1
  - conda-forge::r-markdown=1.1

  ## bioconda packages, see above
  - bioconductor-dupradar=1.14.0
  - bioconductor-edger=3.26.5
  - bioconductor-tximeta=1.2.2
  - bioconductor-summarizedexperiment=1.14.0
  - deeptools=3.3.1
  - fastqc=0.11.8
  - gffread=0.11.4
  - hisat2=2.1.0
  - multiqc=1.7
  - picard=2.21.1
  - preseq=2.0.3
  - qualimap=2.2.2c
  - rseqc=3.0.1
  - salmon=0.14.2
  - samtools=1.9
  - sortmerna=2.1b # for metatranscriptomics
  - star=2.6.1d             # Don't upgrade me - 2.7X indices incompatible with iGenomes.
  - stringtie=2.0
  - subread=1.6.4
  - trim-galore=0.6.4
prefix: /home/USERNAME/scratch/conda/envs/nf-core-rnaseq-1.4.2