This is a simple example for flowr, which preprocess fastq files and aligns using bwa and then merges the output.

requirements

• R (3.2+)
• java (1.7)
• bwa
• samtools
• picard (1.38+)

You may look at the 00_install_deps.sh for some ideas into getting the latest versions of these tools quickly.

git clone https://github.com/flow-r/fastq_bam.git

# rest of the steps assume that this is the WD
cd fastq_bam

# update paths to tools etc.
vi pipe/fastq_bam_bwa.conf

# use FULL paths for reliability, as an example this works too.
fqs1=input/target_brca_example/brca.example.illumina.0.1.fastq
fqs2=input/target_brca_example/brca.example.illumina.0.2.fastq

# by default this will create a flowmat and flowdef
flowr run x=fastq_bam_bwa fqs1=$fqs1 fqs2=$fqs2 samplename=samp

notes

Files 00_install_deps.sh, 01_run_pipe.sh and 02_run_tests.sh are used in automated testing.

These are still a work in progress.