QuickTips

How do I find out if the tool I want to run is already supported by NGSANE

All supported tools have a file in the sampleConfig directory. Browse through there to search for the tool you want to run, then copy the sampleConfig to your project to get started.

How can I use an optional parameter for a program call

Calls of third-party tools have a ADDPARAM variable, as described in the sample config files. Simply define the optional parameters in your project's config file. e.g. BOWTIEADDPARAM="-v 3 -m 1 --tryhard --best --strata --time". To double-check how it is used check back with the actual module file e.g. bowtie.sh to see where the $BOWTIEADDPARAM is incorporated.

RUN_COMMAND="$ZCAT $f | bowtie $RG $BOWTIEADDPARAM $FASTQ_PHRED --threads $CPU_BOWTIE --un $OUTDIR/${n/%$READONE.$FASTQ/.$UNM.fq} --max $OUTDIR/${n/%$READONE.$FASTQ/.$MUL.fq} --sam $BOWTIE_OPTIONS ${FASTA/.${FASTASUFFIX}/} - $OUTDIR/${n/%$READONE.$FASTQ/.$ALN.sam}"

[at this line](at https://github.com/BauerLab/ngsane/blob/master/mods/bowtie.sh#L208)