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Commit 6578eb4b authored by Achisha Saikia's avatar Achisha Saikia
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Merge branch 'aswork' into 'main'

Aswork

See merge request !4
parents a162173d 5c8f8159
Branches fpwork
1 merge request!4Aswork
...@@ -9,12 +9,14 @@ ...@@ -9,12 +9,14 @@
# A unique identifier for the workflow package, text/underscores only # A unique identifier for the workflow package, text/underscores only
name: 'atac-seq-source' name: 'atac-seq-source'
# Who wrote this? # Who wrote this?
author: 'Achisha Saikia, Felix Perez, Peng Lian' author: 'Felix Perez, Achisha Saikia, Peng Lian'
# A contact email address for questions # 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 # A more informative title for the workflow package
title: 'ATAC-seq Source Workflow" 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: | description: |
# TODO: Please describe the workflow. (AS) # TODO: Please describe the workflow. (AS)
......
# ATAC-seq Astrocyte Workflow # 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 ## Requirements
- The ATAC-seq Source workflow ['astrocyte-atac-source] (https://git.biohpc.swmed.edu/s219741/astrocyte-atac-source). - 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), ...@@ -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, '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 ## 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 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 "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME` `caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME`
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/* /*
* Copyright (c) 2024. The University of Texas Southwestern Medical Center * 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 * @authors
* Achisha Saikia, Felix Perez * Felix Perez, Achisha Saikia
* *
*/ */
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