BPIPE GFU PIPELINES

Author: davide.rambaldi AT gmail DOT com

Wiki Documentation

• WIKI HOME
• USER HELP
• DEVELOPERS HELP
• TODO

DIRECTORY STRUCTURE

• bin: scripts
• config: config files
• modules: bpipe modules
• pipelines: bpipe pipelines
• test: test scripts
• templates: script templates
• data: directory for test/scratch data

SCRIPTS

• clean_bpipe_run.sh : cleanup bpipe trash and dirs
• clean_scratch_dir : clean LOCAL_SCRATCH
• pbs_config.sh : generate a bpipe.config file dor PBS professional
• pbs_env.sh : get info about the node environment
• soapsplice_prepare_lane.sh : prepare Illumina lane for alignment with soapsplice
• soapsplice_prepare_align.sh : prepare fastq.gz files for alignment with soapsplice on a node
• verify_bam.sh : verify bam file
• split_fastq.sh : split a fastq file in chunks
• bwa_prepare_single_files.sh : prepare single files for bwa alignment
• htseq_count_prepare_bam.sh : preapre bam for htseq count