Setting VILOCA --windowsize parameter using v-pipe config file not possible

[anikajohn]

The problem

When using the VILOCA rule in v-pipe one can not set the --windowsize parameter directly (through extra in the config file). Instead, in v-pipe's the viloca rule, --windowsize (-w) is set to WINDOW_LEN, which is a function of (I believe) the 3rd column of samples.tsv file. See below (line 389 in snv.smk):

...
if [[ "{params.INSERT_FILE}" == "None" ]]; then
            {params.VILOCA} {params.EXTRA} -t {threads} --mode {params.MODE} -w ${{WINDOW_LEN}} -s {params.SHIFT} -b ${{BAM}} -f ${{REF}} >> $OUTFILE 2> >(tee -a $ERRFILE >&2)
        else
...

Expected behavior

It would be good, if the --windowsize parameter set under extra (see below) would overwrite the ${{WINDOW_LEN}} value. Otherwise, if no 3rd row is specified in samples.tsv, ${{WINDOW_LEN}} is calculated with v-pipe default values and this is not really transparent for the user, who's mainly focused on running VILOCA.

[viloca]
merge_paired_end_reads = false
consensus = false
extra = --NO-strand_bias_filter --min_windows_coverage 1 --windowsize 144

Desktop :

• OS: Linux
• Version: V-pipe 3.0 - prerelease 1, master branch