Moiti001: added workflow image

2021-09-29T12:55:31Z

added workflow image

← Older revision		Revision as of 14:55, 29 September 2021
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	{\|		{\|
	!align="center"\| [[File:~~https://github.com/CarolinaPB/population~~-mapping~~/blob/wur/~~workflow.png~~\|DAG~~]]		!align="center"\| [[File:Population-mapping-workflow.png]]
	\|-		\|-
	\|align="center"\| ''Pipeline workflow''		\|align="center"\| ''Pipeline workflow''
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	== RESULTS ==		== RESULTS ==

	* <run_date>_files.txt dated file with an overview of the files used to run the pipeline (for documentation purposes)		* '''<run_date>_files.txt''' dated file with an overview of the files used to run the pipeline (for documentation purposes)
	* '''processed_reads''' directory with the bam files with the mapped reads for every sample		* '''processed_reads''' directory with the bam files with the mapped reads for every sample
	* '''mapping_stats''' directory containing the qualimap results and a summary of the qualimap results for all samples in <code>sample_quality_summary.tsv</code>		* '''mapping_stats''' directory containing the qualimap results and a summary of the qualimap results for all samples in <code>sample_quality_summary.tsv</code>
	** '''qualimap''' contains qualimap results per sample		** '''qualimap''' contains qualimap results per sample

Moiti001: added info about pipeline

2021-09-29T12:49:30Z

added info about pipeline

New page

Author: Carolina Pita Barros 
Contact: carolina.pitabarros@wur.nl 
ABG 

[https://github.com/CarolinaPB/population-mapping Link to the repository]

== First follow the instructions here: ==

[https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by step guide on how to use my pipelines] 
Click [https://github.com/CarolinaPB/snakemake-template/blob/master/Short%20introduction%20to%20Snakemake.pdf here] for an introduction to Snakemake

== ABOUT ==

This is a pipeline to map short reads from several individuals to a reference assembly. It outputs the mapped reads and a qualimap report.

==== Tools used: ====

* Bwa - mapping
* Samtools - processing
* Qualimap - mapping summary

{|
!align="center"| [[File:https://github.com/CarolinaPB/population-mapping/blob/wur/workflow.png|DAG]]
|-
|align="center"| ''Pipeline workflow''
|}

=== Edit config.yaml with the paths to your files ===

<pre>ASSEMBLY: /path/to/assembly
OUTDIR: /path/to/outdir
PATHS_WITH_FILES:
path1: /path/to/dir</pre>
* ASSEMBLY - path to the assembly file
* OUTDIR - directory where snakemake will run and where the results will be written to. 
If you want the results to be written to this directory (not to a new directory), comment out <code>OUTDIR: /path/to/outdir</code>
* PATHS_WITH_FILES - directory that can contain subdirectories where the '''fq.gz''' reads are located. You can add several paths by adding <code>path2: /path/to/dir</code> under <code>PATHS_WITH_FILES</code>. (The line you add has to have indentation)

The script goes through the subdirectories of the directory you choose under <code>PATHS_WITH_FILES</code> looking for files with '''fq.gz''' extension. 
Example: if <code>path1: /lustre/nobackup/WUR/ABGC/shared/Chicken/Africa/X201SC20031230-Z01-F006_multipath</code>, the subdirectory structure could be:

<pre>/lustre/nobackup/WUR/ABGC/shared/Chicken/Africa/X201SC20031230-Z01-F006_multipath
├── X201SC20031230-Z01-F006_1
│ └── raw_data
│ ├── a109_26_15_1_H
│ │ ├── a109_26_15_1_H_FDSW202597655-1r_HWFFFDSXY_L3_1.fq.gz
│ │ ├── a109_26_15_1_H_FDSW202597655-1r_HWFFFDSXY_L3_2.fq.gz
│ │ └── MD5.txt
│ └── a20_10_16_1_H
│ ├── a20_10_16_1_H_FDSW202597566-1r_HWFFFDSXY_L3_1.fq.gz
│ ├── a20_10_16_1_H_FDSW202597566-1r_HWFFFDSXY_L3_2.fq.gz
│ └── MD5.txt
└── X201SC20031230-Z01-F006_2
└── raw_data
├── a349_Be_17_1_C
│ ├── a349_Be_17_1_C_FDSW202597895-1r_HWFFFDSXY_L3_1.fq.gz
│ ├── a349_Be_17_1_C_FDSW202597895-1r_HWFFFDSXY_L3_2.fq.gz
│ └── MD5.txt
└── a360_Be_05_1_H
├── a360_Be_05_1_H_FDSW202597906-1r_HWFFFDSXY_L3_1.fq.gz
├── a360_Be_05_1_H_FDSW202597906-1r_HWFFFDSXY_L3_2.fq.gz
└── MD5.txt </pre>
== RESULTS ==

* **<run_date>_files.txt** dated file with an overview of the files used to run the pipeline (for documentation purposes)
* '''processed_reads''' directory with the bam files with the mapped reads for every sample
* '''mapping_stats''' directory containing the qualimap results and a summary of the qualimap results for all samples in <code>sample_quality_summary.tsv</code>
** '''qualimap''' contains qualimap results per sample

Population mapping pipeline - Revision history

Moiti001: added workflow image

Moiti001: added info about pipeline