They require certain files to exist, depending on which phases of the pipeline you are running. Pipelines generated to explore the BDS language. The scripts provide exampels of file parsing, dependency processing, and cluster exectuion.
bam/ Do not share; Files created here
ref/ Sharable: Read-Only
fastq/ Do not share; Files created here
- Phase 0: The pipeline starts with an original BAM file, located in the BAM directory.
- Phase 1: Reassembling the FASTQ files from the provided BAM file.
- Phase 2: Generating a new BAM file, "_realigned.BAM", from the FASTQ files.
- Phase 3: Sorting the newely generated BAM file "_realigned.BAM" to make "_realigned_sorted.BAM"
- Phase 4: Indexing of "_realigned_sorted.BAM" to produce "_realigned_sorted.bam.bai"
The original BAM file used to generate this pipeline from sratch, is located on Genesis here: /bam/Pfeiffer.bam
The original .FA file used as a reference in this pipeline, it is a symlink and is located on Genesis here: /ref/GRCh37-lite.fa
For the purpose of this pipeline, it is permitted to symlink to these files.