Tool core parameters

Found in file: scripts/config.sh

Note

If a parameter is recommended as a default. It’s for the snakemake workflow to work smooth. Parameters with this value will be marked with: recommended to leave at default

Warning

If a parameter exists in the config files but isn’t listed in this reference, please don’t change the default on this paramenter.

Basic parameters

ncores: Number of cores or threads that each tool will use. Note when using a snakemake pipeline: the resulting number of cores used is a result of multiplication of ncores and snakemake -j parameter.

Default: 16
workdir recommended to leave at default: Name of the base directory inside the Docker.

Default: /MOUNT
outdir recommended to leave at default: Name of the output directory; should be named after the specific tool that was used (use the $tool variable for that).

Default: $workdir/output/${tool:-unspecific}-output
read_length: Length of the reads inside the fastq files.

Default: 76

Input Directories

inputdir recommended to leave at default: Base input directory.

Default: $workdir/input
controlfolder recommended to leave at default: Directory for all needed input files when no differential comparison. Directory for control sample input files when running differential AS event detection.

Default: $inputdir/controldir
casefolder recommended to leave at default: Directory only for case sample input files in case of differential AS event detection.

Default: $inputdir/casedir
fastqdir recommended to leave at default: Directory for fastq files.

Currently same as ‘controlfastq’

Default: $controlfolder/fastqdir
bamdir recommended to leave at default: Directory for bam files.

Currently same as ‘controlbam’

Default: $controlfolder/bamdir
samdir recommended to leave at default: Directory for sam files.

Default: $controlfolder/bamdir
fastadir: Directory for the reference genome file

Default: $inputdir
gtfdir: Directory for the annotation file file.

Default: $inputdir
gffdir: Directory for gff file

Default: $inputdir

Tool specific parameters

bowtie_fastadir: Some tools require chromosome-wise fasta-inputs

Default: $inputdir/fasta_chromosomes/

Index Parameters

recompute_index: Force recompute the index even if the index with $indexname already exists.

Default: false
indexname: Basename of the index (without eg. .1.bt2 for bowtie index).

Default: ${fastaname}_index
star_index: Folder containing a star index built with the $gtf and $fasta files (see below), used by: IRFinder, KisSplice, rMATS

Default: $workdir/index/star_index
indexdir: Directory of the index.

Default: $workdir/index/${tool:-unspecific}_index

ASimulatoR Parameters

asimulator_gtf: Name of the file in the input directory used by ASimulatoR to generate new transcripts

Example: Homo_sapiens.GRCh38.105.gtf

Input Parameters

fastaname: Name of the genome reference file (fasta format) inside $fastadir.

Example: Homo_sapiens.GRCh38.dna.primary_assembly.fa
gtfname: Name of annotation reference file inside $gffdir.

Example: splicing_variants.gtf
gffname: Name of gff reference file inside $gffdir.

Example: splicing_variants.gff3

Note

There should be no need to edit fasta, gtf and gff since they just combine other parameters.
fasta: Full path to the reference genome file.

Default: ${fastadir:-unspecific}/$fastaname
gtf: Full path to the annotation file.

Default: ${gtfdir:-unspecific}/$gtfname
gff: Full path to the gff file.

Default: ${gffdir:-unspecific}/$gffname

Basic Mapping Parameters

outname recommended to leave at default: Base name of the output files. They will usually be prefixed with the fastq file name and suffixed with .sam.

Default: $tool (the name of the tool creating the ouput files)

Warning

Something broke while changing the config file? Make sure there is no space between the variable, the equal sign and the value.

Since these files are bash scripts, it is important to mind the syntax rules. E.g., there can’t be a whitespace before and after “=”.

For example: | Wrong: workdir = “dockers/” | Right: workdir=”dockers/”