add make_igv_bams pl
remove rookie error calling wrong script
generalise ws location in km_pipeline
update sort_index_bam.sh
add tophat pipeline
fix a few small bugs in tophat
remove old cutadapt script
updates and bugfixes to pairwise edgeR script
fix glob bugs in qc scripts
add edgeR script to kmpipeline runner
add subjunc aligner script
cat script files into logs in km_pipeline
cat script files into logs in pete 277 pipeline
rename km_pipeline to km_pairwise, and make the runner script run the pairwise edgeR exact test script
add km_glm pipeline
fix weird samtools crash when sorting piped bam in subread/junc
fix typo in pairwise edgeR script location
add work-around for samtools sort -f bug
add edgeR to pete's 277 runner script
fix extraneous mkdir -p in runner script