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environment.yml
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environment.yml
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# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-rnaseq-1.3
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- fastqc=0.11.8
- trim-galore=0.5.0
- star=2.6.1d # don't upgrade me - 2.7X indices incompatible with iGenomes.
- hisat2=2.1.0
- picard=2.18.27
- bioconductor-dupradar=1.12.1
- conda-forge::r-data.table=1.12.0
- conda-forge::r-gplots=3.0.1.1
- bioconductor-edger=3.24.1
- conda-forge::r-markdown=0.9
- csvtk=0.17.0
- preseq=2.0.3
- rseqc=3.0.0
- samtools=1.9
- stringtie=1.3.5
- subread=1.6.4
- gffread=0.9.12
- deeptools=3.2.0
- multiqc=1.7
- bioconda::salmon=0.13.1
- bioconda::htseq=0.11.2