Roadmap

Big picture

First, see this PDF.

There are 2 project targets.

1. Enabling the bio tools RPM packages on x86_64, ppc64le and aarch64, optionally other CPU architectures for Fedora and Extra Packages for Enterprise Linux (EPEL) 7 and 8. The RPM packages are maintained on Fedora dist-git repositories, and listed up on the Fedora Koschei biology tag group [1] linked from Fedora Medical Special Interest Group (SIG) page [2].
2. Enabling the nf-core pipelines on ppc64le and aarch64 based HPCs, benchmarking it.

We use the following nf-core pipelines. First 3 pipelines are essential. Others are certainly relevant. We repeat the first and second target for each pipeline in order in an agile manner.

• nf-core/nanoseq: Nanopore sequencing analysis
• nf-core/artic: COVID-19 analysis
• nf-core/viralrecon: COVID-19 analysis
• nf-core/scrnaseq: Single-cell analysis
• nf-core/smartseq2: Single-cell analysis
• nf-core/sarek: Whole-genome analysis
• nf-core/mag: Meta-genomics analysis
• nf-core/bcellmagic: Immune response analysis

Working status

WIP means Working In Progress.

1. Prepare

• 1.1. List up the dependency software of nf-core pipelines. [DONE]
• 1.2. Release existing used bio tools RPM packages to RHEL 8 and 7. [DONE]
• 1.3. Try to run this tutorial for COVID-19 analysis. [WIP]

2. Support nf-core piplines on ppc64le and aarch64

• 2.1. nf-core/nanoseq
  • 2.1.1. Run nf-core/nanoseq on local.

References

• [1] https://koschei.fedoraproject.org/groups/biology?untracked=1
• [2] https://fedoraproject.org/wiki/SIGs/Medical