Container

[BarryDigby]

The workflow requires multiple tools to be added to the Docker container. Update the environment.yml file accordingly and make sure the container passes the continuous integration tests in your own repository before making a PR against thedev branch at BarryDigby/rtp_workshop.

Be patient while conda solves the environment. Passing multiple tools to the environment.yml file can take a while to build.

Quality Control

• fastqc
• multiqc
• qualimap
• rseqc
• samtools
• bbtools (for bbduk.sh)

Miscellaneous

• gffread
• bedops
• bedtools

Alignment

• star=2.6.1d
• hisat2
• stringtie
• salmon
• kallisto