snakeflow's Introduction

snakeflow

My NGS workflows based on snakemake

workflows include:

RNA-seq (Salmon,hisat2)
ChIP-seq (MACS2)
ATAC-seq (MACS2)
CITE-seq (Antibody captured, 10X genomics)
Germline SNV calling (GATK, BCFtools)
Germline Structural Variant calling
- short-read: Speedseq + svtools
- long-read:
  - Pacbio: ngmlr/minimap2 + sniffiles

Dependency

General
- samtools, deeptools, bedtools
- fastqc, rseqc, multiqc, fastp
- graphviz
python 3
- numpy
- pandas
- snakemake
- matplotlib
- seaborn
- gseapy
- macs2
- rseqc
R
- DESeq2
- tximport
- readr
- pheatmap
- ggplot2
- ggrepel
- clusterProfiler
- ChIPSeeker
- EnsDb.Hsapiens.v86
Variant calling
- GATK (> 4.0)
- BCFtools
- Speedseq + svtools
- minimap2
- ngmlr
- sniffiles
RNA-seq
- hisat2, salmon
- rMATS-turbo, rmats2sashimiplot
Single cell genomics

cellranger

Installation

Set up running environment. This config file will create a python 3.x env.

bash snakeflow-enviroment-setup.sh

usage

# Step1: activate snakemake
source activate snakeflow

# Step2: clone this repo

# Step3: copy all your fastq files into fastq dir
find . -name "*fastq.gz" | while read id; do cp $id fastq/; done;

# Step4: modify config.yml with your own paramter
# Note: put config.yml in the same dir with your snakefile.
vim  config.yml

# Step5: run snakemake with -np option. this test your ``commands`` runs without any errors.
snakemake -s salmon-tximport-deseq2-v0.2.snakefile -np

# Step6: export workflow charts
snakemake -s salmon-tximport-deseq2-v0.2.snakefile --dag | dot -Tpdf > dag.pdf

# Step7: or using the default snakemake environment you've created above.
snakemake -s salmon-tximport-deseq2-v0.1.snakefile -p -j 8

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