CITATION.cff

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
---
cff-version: 1.2.0
title: "HPC Workflow Management with Snakemake"
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Alan
    family-names: O'Cais
    email: "alan.ocais@cecam.org"
    affiliation: "University of Barcelona"
    orcid: "https://orcid.org/0000-0002-8254-8752"
    alias: ocaisa
  - given-names: Andrew
    family-names: Reid
    email: "andrew.reid@nist.gov"
    affiliation: "National Institute of Standards and Technology"
    orcid: "https://orcid.org/0000-0002-1564-5640"
    alias: reid-a
  - given-names: Annajiat
    family-names: Alim Rasel
    email: "annajiat@bracu.ac.bd"
    affiliation: "Brac University"
    orcid: "https://orcid.org/0000-0003-0198-3734"
    alias: annajiat
  - given-names: Benson
    family-names: Muite
    email: "benson_muite@emailplus.org"
    affiliation: "Kichakato Kizito"
    alias: bkmgit
  - given-names: Trevor
    family-names: Keller
    email: "trevor.keller@nist.gov"
    affiliation: "National Institute of Standards and Technology"
    orcid: "https://orcid.org/0000-0002-2920-8302"
    alias: tkphd
  - given-names: Wirawan
    family-names: Purwanto
    email: "wpurwant@odu.edu"
    affiliation: "Old Dominion University"
    orcid: "https://orcid.org/0000-0002-2124-4552"
    alias: wirawan0

repository-code: "https://github.com/carpentries-incubator/hpc-workflows"
url: "https://carpentries-incubator.github.io/hpc-workflows/"
abstract: >-
  When using HPC resources, it's very common to need to
  carry out the same set of tasks over a set of data
  (commonly called a workflow or pipeline). In this lesson
  we will make an experiment that takes an application which
  runs in parallel and investigate its scalability. To do
  that we will need to gather data, in this case that means
  running the application multiple times with different
  numbers of CPU cores and recording the execution time.
  Once we've done that we need to create a visualisation of
  the data to see how it compares against the ideal case.

  We could do all of this manually, but there are useful
  tools to help us manage data analysis pipelines like we
  have in our experiment. In the context of this lesson,
  we'll learn about one of those: Snakemake.
keywords:
  - HPC
  - Carpentries
  - Lesson
  - Workflow
  - Pipeline
license: "CC-BY-4.0"
references:
  - title: "Getting Started with Snakemake"
    authors:
      - family-names: Collins
        given-names: Daniel
        alias: DC23
    type: software
    repository-code: "https://github.com/carpentries-incubator/workflows-snakemake"
    url: "https://carpentries-incubator.github.io/workflows-snakemake/"
  - title: "Snakemake for Bioinformatics"
    authors:
      - family-names: Booth
        given-names: Tim
        alias: tbooth
        orcid: "https://orcid.org/0000-0003-2470-9519"
    type: software
    repository-code: "https://github.com/carpentries-incubator/snakemake-novice-bioinformatics/"
    url: "https://carpentries-incubator.github.io/snakemake-novice-bioinformatics"