DNAseq pipeline

a DNAseq mapping pipeline from .fastq files to .bam files with intermediate quality reports

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set up pipeline

before running, you have to set up the attached Docker image:

docker build -t dnaseq-pipeline https://raw.githubusercontent.com/loipf/DNAseq-pipeline/master/docker/Dockerfile

now either replace the Docker container hash (last output line from previous build command) in nextflow.config or run nextflow with the -with-docker dnaseq-pipeline argument.

if you already have an reference genome, you can specify it with the nextflow argument --reference_genome [genome.fa] or in the main.nf file. otherwise run the following script to download it into data folder:

bash scripts/data_acquisition.sh

additional, an 3' and 5' adapter sequence (file) needs to be specified with the nextflow arguments --adapter_3_seq_file [sequence|file.fasta] and --adapter_5_seq_file [sequence|file.fasta] or in the main.nf file. if a file is provided, it must be structured like the following example:

> adapter_3_batch_01
AANTGG
> adapter_3_batch_02
GATCGG

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run mapping pipeline

it can be run locally with downloaded github-repo and edited nextflow.config file with:

nextflow run main.nf

or

nextflow run loipf/DNAseq-pipeline -r main --project_dir /path/to/folder --reads_dir /path/to/samples --num_threads 10 --adapter_3_seq_file adapter_3.fasta --adapter_5_seq_file adapter_5.fasta --reference_genome genome.fasta -with-docker dnaseq-pipeline

for this execution to work properly, you have to be in the current project directory.

optional extendable with:

-resume
-with-report report_DNAseq-pipeline
-with-timeline timeline_DNAseq-pipeline
-w work_dir

by default, all output will be saved into the data folder of the current directory