Author: davide.rambaldi AT gmail DOT com
- bin: scripts
- config: config files
- modules: bpipe modules
- pipelines: bpipe pipelines
- test: test scripts
- templates: script templates
- data: directory for test/scratch data
- 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