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nf-wgs-dsl2

Running PathWeaver

After running the WGS nextflow pipeline or the QC workflow, you may want to run PathWeaver to interpret your results.

Set up

To set up Pathweaver, copy the PathWeaver workflow from Arwen /data/general/finterly/pathweaver_run to the desired location.

PathWeaver Input

1. Run Name

Given a string run name, the PathWeaver workflow will create a new subdirectory in the pathweaver_run directory with the given string and output all results to that new subdirectory.

2. Bam Files Directory

PathWeaver works with the QC outputs from final_bams directory:

  • .dup.pf.bam : the final pf bam file
  • .dup.pf.bam.bai : index for pf bam file

Copy these files to a single directory

3. Genes List

PathWeaver will run on a given genes list, simple text file list, example below:

gene_list.txt

PF3D7_0304600
PF3D7_0315200
PF3D7_1335900

Running PathWeaver

The following command will run PathWeaver

bash final_run_pathweaver_2024_07_30.sh <run_name> <bam_dir> <gene_list>

For example:

bash final_run_pathweaver_2024_07_30.sh \
test_run \
path/final_bam_dir \ 
gene_list.txt

Recommend running PathWeaver on Arwen using tmux. A log will print out as PathWeaver runs.

Running PathWeaver Analysis / Plots

To generate plots for your pathweaver output

  1. open the generate_plots_2024_07_30.Rmd in RStudio and edit the run_dir params in the R notebook header (shown below) to the path of your PathWeaver run output directory. Then simply run the R notebook! Some adjustments may be needed for different analysis!
---
title: "R Notebook"
output: 
params:
  run_dir: "/home/me/pathweaver_run/test_run"
---