Running Wochenende

Running nf_wochenende

1 First follow the installation Wiki page to set up the pipeline and paths to resources properly

2 Get one of more fastq files in the current directory to analyze

• Get a small read fastq file as input (present in the repo for testing)
• At present, Wochenende needs uncompressed fastq files with sample names like sputum_R1.fastq and sputum_R2.fastq to run correctly. So please rename your files.
• gunzip *.fastq.gz
• rename 's/_001//g' *.fastq
• Now check your files look like sample_details_R1.fastq

3 Edit the parameters you'd like to use in the start_nf.sh file (or use the defaults)

• Edit start_nf.sh
• Note - we strongly recommend bwa mem for single ended Illumina data, minimap2 for paired end short read data, and minimap2 for long read data
• Please do not use bwa mem for paired end data, since the alignments can be very poor (soft-clipping problems)

4 Start Wochenende

• Run bash start_nf.sh

See our Wiki page on interpreting the output after data has been produced.