Bioinformatics-Pipelines

Bioinformatics pipelines developed either using Nextflow or Snakemake.

Snakemake Pipelines

• The Snakemake directory has different Snakemake pipelines developed for different data types.
• Each directory contains the Snakemake file for that respective workflow and also a Discussion.Rmd which contains information about what references and methods were used to recreate the results via the pipeline and what the conclusions/learning outcomes were.
• The directory also includes other scripts written outside of Snakemake (using either Python or R) which were used for further analysis of the data.
• Where relevant there is an "images" directory present which holds the images generated during downstream analysis of the data.
• The conda env used to run each workflow is present and additionally there is an envs repository with the yml used for each tool during analysis.

Links to Snakemake files

1. Snakemake RNASeq:
   • Methods and Results
2. Snakemake ChIPSeq:
   • Methods and Results
   • Images obtained from downstream analysis
3. Snakemake ATACSeq:
   • Methods and Results
   • Images obtained from downstream analysis

Nextflow Pipelines

The Nextflow pipelines were developed using the same workflow to additionally practice Groovy and are stored in Nextflow. Since the same methods and data were used, the results are identical. The links for the pipelines can be found below:

1. NF RNASeq
2. NF ChIPSeq