Snakemake Workflow for ATAC-Seq Data Analysis: Replicating Bioinformatics Analysis

public public 1yr ago 0 bookmarks
View Workflow
Report
projet_cloud
projet_cloud
View Workflow

TP Snakemake

The goal of this project is the initiation to a workflow language Snakemake and the discovery of its interest compared to the construction of a rudimentary workflow built in bash.

The project is based on the construction of a workflow in Snakemake allowing to reproduce the analysis steps conducted in the ATACseq project from the quality control of the fastq.gz sequences to the identification of regions of accessibility to the DNA in 2 biological conditions considered. Due to the impossibility to instantiate a VM with the BioPipes image (the cloud) and to install Snakemake on the Mesocenter compute cluster, I could not properly debug my snakemake script.

The snakemake workflow corresponds to the Snakefile and the configuration files are config.yaml and env.yaml for the working environment.

Code Snippets

16
17
18
19
20
shell:
	"""
	mkdir -p tmp
	gunzip -c {input} > {output}
	"""
SnakeMake From line 16 of main/Snakefile 
31
32
33
34
35
shell:
	"""
	mkdir -p results/fastqc_init
	fastqc {input} -o "results/fastqc_init" -t {threads}
	"""
SnakeMake FastQC From line 31 of main/Snakefile 
48
49
50
51
52
53
54
shell:
	"""
	mkdir -p results/cutadapt
	cutadapt -j 1 -a R1=CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A R2=CTGTCTCTTATACACATCTGACGCTGCCGACGA \
	--output={output} --paired-output={output} --error-rate0.1 --times=1 --overlap=3 --minimum-length=20 --pair-filter=any --quality-cutoff=20 \
	-j {threads} {input}
	"""
SnakeMake Cutadapt From line 48 of main/Snakefile 
67
68
69
70
71
72
shell:
	"""
	mkdir -p results/bowtie2
	bowtie2 --very-sensitive -p {threads} -k 10 -x {input.genome} -1 {input.r1} -2 \
	| samtools view -q 2 -bs - | samtools sort - -o {output}
	"""
SnakeMake SAMtools Bowtie 2 From line 67 of main/Snakefile 
83
84
85
86
shell:
	"""
	samtools index -b {input.bam}
	"""
SnakeMake SAMtools From line 83 of main/Snakefile 
94
95
96
97
shell:
	"""
	samtools idxstats {input} > {output}
	"""
SnakeMake SAMtools From line 94 of main/Snakefile 
107
108
109
110
111
112
113
114
shell:
	"""
	java -jar /opt/apps/picard-2.18.25/picard.jar MarkDuplicates \
	I={input} \
	O={output.bam} \
	M={output.met} \
	REMOVE_DUPLICATES=true
	"""
SnakeMake Picard From line 107 of main/Snakefile 
122
123
124
125
shell:
"""
samtools index -b {input}
"""
SnakeMake SAMtools From line 122 of main/Snakefile 
133
134
135
136
shell:
"""
samtools idxstats {input} > {output}
"""
SnakeMake SAMtools From line 133 of main/Snakefile 
149
150
151
152
shell:
	"""
	macs2 callpeak -t {input.cult_24h} -c {input.cult_0h} -f BAM -g 'mm' -n
	"""
SnakeMake macs2 From line 149 of main/Snakefile
ShowHide 5 more snippets with no or duplicated tags.

Login to post a comment if you would like to share your experience with this workflow.

Do you know this workflow well? If so, you can request seller status , and start supporting this workflow.

Free

Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/embusefala/Projet_Cloud
Name: projet_cloud
Version: 1
Badge:
workflow icon

Insert copied code into your website to add a link to this workflow.

Downloaded: 0
Copyright: Public Domain
License: None
  • Future updates

Related Workflows

psychip_snakemake
Show Details View Workflow
ENCODE pipeline for histone marks developed for the psychENCODE project
public

public

psychip pipeline is an improved version of the ENCODE pipeline for histone marks developed for the psychENCODE project. The o...
raw sequence reads Alignment Sequence alignment report macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
ncov_2
Show Details View Workflow
Near-real time tracking of SARS-CoV-2 in Connecticut
public

public

Repository containing scripts to perform near-real time tracking of SARS-CoV-2 in Connecticut using genomic data. This pipeli...
JSON nextclade Augur Biopython FOCUS Pandas Snakemake bs4 epiweeks geopy matplotlib numpy pycountry pycountry-convert uszipcode
Free
28
cellranger-snakemake-gke
Show Details View Workflow
snakemake workflow to run cellranger on a given bucket using gke.
public

public

A Snakemake workflow for running cellranger on a given bucket using Google Kubernetes Engine. The usage of this workflow ...
macs2 ucsc-bedclip bedGraphToBigWig BEDTools BWA Picard SAMtools Snakemake
Free
74
atlas
Show Details View Workflow
ATLAS - Three commands to start analyzing your metagenome data
public

public

Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads Genome assembly Annotation track checkm2 gunc prodigal snakemake-wrapper-utils MEGAHIT Atlas BBMap Biopython BioRuby Bwa-mem2 cd-hit CheckM DAS Diamond eggNOG-mapper v2 MetaBAT 2 Minimap2 MMseqs MultiQC Pandas Picard pyfastx SAMtools SemiBin Snakemake SPAdes SqueezeMeta TADpole VAMB CONCOCT ete3 gtdbtk h5py networkx numpy plotly psutil utils metagenomics
Free
175
rna-seq-star-deseq2
Show Details View Workflow
RNA-seq workflow using STAR and DESeq2
public

public

This workflow performs a differential gene expression analysis with STAR and Deseq2. The usage of this workflow is described ...
raw sequence reads Gene expression profiling ID list snakemake-wrapper-utils biomaRt PCAtools BiocParallel BWA Cutadapt DESeq2 GFFutils MultiQC Pandas SAMtools Snakemake STAR cli stringr tidyverse RNA-Seq
Free
41
dna-seq-gatk-variant-calling
Show Details View Workflow
This Snakemake pipeline implements the GATK best-practices workflow
public

public

This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
VCF raw sequence reads Variant calling genetic variants gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BWA FastQC MultiQC Pandas Picard SAMtools Snakemake Trimmomatic Variant Effect Predictor (VEP) common matplotlib numpy seaborn DNA
Free
57