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#Supported in both Firefly and Falco
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rnaseq-process    RNA-seq QC, Align, and RSEM for FASTQ files
rnaseq-merge      Merge rnaseq-process results for downstream analyses
rnaseq-de         Perform DE analysis using DESeq2
rnaseq-summary    Summarize RNA-Seq DE results

rnaseq-var        RNA-seq variant calling pipeline
rnaseq-motif      RNA-seq TFBS motif finding pipeline
rnaseq-motif-summary  RNA-seq TFBS motif finding results summary	
motif-finder      Transcription factor binding motif prediction

chipseq-process   ChIP-seq/ATAC-Seq QC, Align, and Peak Calling
chipseq-merge     Summarize ChIP-Seq results
chipseq-de        Perform DE analysis for ChIP-Seq
chipseq-summary   Summarize ChIP-seq DE results

dnaseq-process    DNA-Seq (Exome/Genome-Seq) processing based on GATK4

mergefiles        Use a model file to merge different files together
text2excel        Build excel file using text file (by Andrew Hodges)

gsea-gen          Generate files ready for GSEA analysis

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#Supported only in Firefly
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parallel-job      Batch job submission in Firefly

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#Supported only in Falco
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bs-fastq          Download and merge FASTQ files from Basespace	
ensembl2ucsc      Convert Ensembl gtf/fasta/bed into UCSC format
geo-download      Download raw FASTQ files from GEO