Updated description part 2

astrocyte_pkg.yml

@@ -9,12 +9,14 @@
 # A unique identifier for the workflow package, text/underscores only
 name: 'atac-seq-source'
 # Who wrote this?
-author: 'Achisha Saikia, Felix Perez, Peng Lian'
+author: 'Felix Perez, Achisha Saikia, Peng Lian'
 # A contact email address for questions
-email: 'achisha.saikia@utsouthwestern.edu, felix.perez@utsouthwestern.edu, biohpc-help@utsouthwestern.edu'
+email: 'felix.perez@utsouthwestern.edu, achisha.saikia@utsouthwestern.edu, biohpc-help@utsouthwestern.edu'
 # A more informative title for the workflow package
 title: 'ATAC-seq Source Workflow"
-# A summary of the workflow package in plain text
+
+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.
+
 description: |
   # TODO: Please describe the workflow. (AS)
 

docs/index.md

@@ -8,7 +8,7 @@ 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) -->
+<!-- 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.