# Template for human RNA-seq using Illumina prepared samples
---
details:
  - analysis: RNA-seq
    genome_build: GRCh37
    algorithm:
      aligner: tophat2
      trim_reads: read_through
      adapters: [truseq, polya]
      strandedness: unstranded
upload:
  dir: ../final

# Template for human RNA-seq using Illumina prepared samples
---
details:
  - analysis: RNA-seq
    genome_build: GRCh37
    algorithm:
## for hg38, change the aligner to hisat2
      aligner: star
## uncomment below if adapter trimming needs to be performed
## most samples will not need this
#      trim_reads: read_through
#      adapters: [truseq, polya]
## uncomment below if strandedness needs to be set
#      strandedness: unstranded
## uncomment below if fusion calling is necessary
#      fusion_caller: [pizzly, oncofuse]
## uncomment below if variant calling is necessary, vardict also supported
#      variantcaller: [gatk-haplotype, vardict]
## uncomment below if you want other expression callers, salmon is run by default
#      expression_caller: [cufflinks, express, stringtie, sailfish, dexseq, kallisto, salmon]
## uncomment below if you want to provide a custom transcriptome FASTA file
#      transcriptome_fasta: your-transcriptome.fa
## uncomment below if you want to provide a custom transcriptome GTF file
#      transcriptome_gtf: your-transcriptome.gtf
## uncomment below if you want to want to provide a FASTA file of spikeins to quantify
#      spikein_fasta: your-spikein.fa
upload:
  dir: ../final

Update RNA-seq template with inline options.
Update RNA-seq template with inline options.

Thanks to @skanwal for pointing out this is confusing for
onboarding new users.
