Replace the shell block with a script block in the runSource process.

docs/index.md

@@ -8,7 +8,6 @@ This repo is used to wrap the existing ATAC-seq pipeline listed below (Runner),
 - The ATAC-seq Runner workflow, 'astrocyte-atac-runner] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-runner). This repo contains the original ATAC-seq pipeline developed by the ENCODE team.
 
 ## The ATAC-seq Runner workflow
-<!-- TODO: Fill out intro to ATAC-seq pipeline. Which commands do we use to run this pipeline? What will the NextFlow script use? (AS) (DONE)-->
 
 This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq. The pipeline can be run end-to-end, starting from raw FASTQ files all the way to peak calling and signal track generation using a single caper submit command. One can also start the pipeline from intermediate stages (for example, using alignment files as input). The pipeline supports both single-end and paired-end data as well as replicated or non-replicated datasets. The outputs produced by the pipeline include 1) formatted HTML reports that include quality control measures specifically designed for ATAC-seq and DNase-seq data, 2) analysis of reproducibility, 3) stringent and relaxed thresholding of peaks, 4) fold-enrichment and pvalue signal tracks.