Pixel distance in Picard mark duplicates

[trombitomi]

Description of the bug

the following piece of code did not behave as expected:

if (params.sequencer=="NovaSeq") {
        opt_dupl_dist = 12000
    } else if (params.sequencer="HiSeq") {
        opt_dupl_dist = 2500
    } else { opt_dupl_dist = 100 }

in params.yaml, I defined:

sequencer: "NextSeq"

yet, the submitted command:

...
--OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 \
...

I propose a little update:

if (params.sequencer=="NovaSeq") {
        opt_dupl_dist = 12000
    } else if (params.sequencer="HiSeq") {
        opt_dupl_dist = 2500
    } else if (params.sequencer="NextSeq") {
        opt_dupl_dist = 100
    } else { error "Error: Specify sequencer (NextSeq, HiSeq, NovaSeq)" }

Command used and terminal output

...
WARN: `params.sequencer` is defined multiple times -- Assignments following the first are ignored
...

Relevant files

No response

System information

VSC_HPC_UGent Tier2