help_msg.txt

Special (may replace parameters that are otherwise Required)
  -c, --config			A valid configuration file, each line of which specifies R1 fastq files, optionally comma delimited with a second entry for final file name prefix. A # commented header is also allowed with lines that start with #CMD being parsed for command line parameters.  The config file can specify all required and optional parameters in this way.
  -ref, --reference		Path to parent directory for all reference components
  
Required
  -o, --outDir			Relative or absolute path where pipeline results shuold be written.
  -idx, --starIndex		Path to STAR index, will be derived from -ref if not supplied.
  -s, --suppaRef		Path to SUPPA2 ioi and ioe references, will be derived from -ref if not supplied.
  -g, --gtf			Path to GTF reference file, will be derived from -ref if not supplied.
  -fa, --fasta			Path to genome fasta file, will be derived from -ref if not supplied.

Optional
  -f1s, --f1_suffix		<_R1_001.fastq.gz> The suffix used for R1 fastq files.  This suffix will be replaced with the R2 suffix to guess R2 fastq files.  If no final file prefix is supplied, removal of the R1 suffix generates the final file prefix.
  -f2s, --f2_suffix		<_R2_001.fastq.gz> The suffix used for R2 fastq files.  Will replace the R1 suffix when guessing R2 files.
  -i, --inDir			<current directory> The directory in which all fastq files are located.
  -rDNA, --rDNA_starIndex	Path to STAR index for organism's rDNA, will be derived from -ref if not supplied.  Without a rDNA STAR index, the rDNA alignment step is skipped.
  -SE, --SE			If activated, alignment will be in single-end mode instead of the default of paired-end.
  -noSub, --noSub		If activated, bash will be used to run all pipeline steps in serial instead of sbatch to run in parallel via the job scheduler.  For debugging only or if SLURM's sbatch is not available.
  -p, --pipeline 		Alternative pipeline scripts.  Typically if only a portion of pipeline is required.
  -docker, --docker Docker container to use for running the entire pipeline.