Merge branch 'aswork' into 'main'

Aswork

See merge request !4

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

 # ATAC-seq Astrocyte Workflow
 
-<!-- TODO: Fill out intro (AS) -->
+ATAC-seq is a bioinformatics best-practice analysis pipeline used for ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) data analysis. It is built upon the ENCODE ATAC workflow written in workflow description language (wdl) and uses Nextflow to run in the astrocyte platform.
 
 ## Requirements
 - The ATAC-seq Source workflow ['astrocyte-atac-source] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-source).
@@ -8,7 +8,9 @@ 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.
 
 On HPC, make sure that Caper's conf ~/.caper/default.conf is correctly configured to work with HPC. The following command will submit Caper as a leader job to SLURM with Singularity
 `caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME`

workflow/main.nf

 /*
  * Copyright (c) 2024. The University of Texas Southwestern Medical Center
  *
- * TODO: (AC) Brief description of ATAC-seq
- *
+ * TODO: (AC) Brief description of ATAC-seq (DONE)
+ * ATAC-seq is a molecular biology technique that assesses chromatin accessibility in a genome. It uses a hyperactive Tn5 transposase to insert sequencing adapters into open chromatin regions, allowing researchers to identify and sequence these accessible genomic regions. ATAC-seq is widely used to study gene regulation, identify enhancers and promoters, and gain insights into chromatin structure.
  * @authors
- * Achisha Saikia, Felix Perez
+ * Felix Perez, Achisha Saikia
  *
  */