Quantification (Short-read)

Quantify RNA in short-read RNA sequencing FASTQ files

tools

The following tools run by default (methods: "all"):

kallisto, salmon

usage

nexus run --nf-workflow quantification_short-read.nf -params-file params.yaml

Note

Nextflow config files are available here. Use the config file that matches your installed nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

Download params.yaml

# =============================================================================
# params.yaml — quantification_short-read
#
# Usage:
#   nextflow run quantification_short-read.nf -params-file params.yaml
#
# Fill in the required fields below. Optional fields can be left at their
# defaults or removed entirely.
# =============================================================================


# -----------------------------------------------------------------------------
# Required
# -----------------------------------------------------------------------------

# TSV file with columns:
#   sample_id
#   fastq_file_1
#   fastq_file_2
samples_tsv_file: ""

# Directory to which output files will be copied
output_dir: ""

# Reference transcripts FASTA file
reference_transcripts_fasta_file: ""


# -----------------------------------------------------------------------------
# Optional — general
# -----------------------------------------------------------------------------

# Methods to run. Comma-separated list or 'all'.
# Allowed values:
#   all, kallisto, salmon
methods: "all"


# -----------------------------------------------------------------------------
# Kallisto (paired-end mode)
# Optional arguments.
# -----------------------------------------------------------------------------
kallisto:
  # Extra CLI arguments passed directly to kallisto quant.
  quant_extra_args: ""


# -----------------------------------------------------------------------------
# Salmon
# Optional arguments.
# -----------------------------------------------------------------------------
salmon:
  # Extra CLI arguments passed directly to salmon index.
  index_extra_args: "--gencode"

  # Extra CLI arguments passed directly to salmon quant.
  quant_extra_args: "--libType IU --seqBias --gcBias --posBias"