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Change Launch_Casava.sh to demux by lane (remove --no-lane-splitting) and then at the end of the process concatenate and write R1 & R2 for archiving/delivery

Documentation Needed to Start

Document all assays processed by IGO and their pipeline steps and review RECIPE list at https://github.com/mskcc/fastq-plus/blob/master/Automate-Stats/Launch_Stats_GRCh37.sh

Most Common Assays Pipeline (WES, IMPACT, RNASeq)

Generate GATK best practices bam creation similar to https://github.com/nf-core/sarek/blob/master/main.nf:

Input is one samplesheet, for each unique sample map to reference Merge bams Do the rest of GATK best practices https://gatk.broadinstitute.org/hc/en-us/articles/360035535912-Data-pre-processing-for-variant-discovery Then call IGO Picard stats:

Then fingerprinting:

Testing

Create small test datasets (SeqTK or use top-up reads to find small fastqs):

WES TODO find projects IMPACT RNASeq