Hello, I am trying to add -qc-options to adjust the trimmomatic parameters in the biobakery wmgx workflow. I am hoping to trim my sequences and was successful using the “trimmomatic-options=TRAILING:3” when just using kneaddata alone, but as I have 140 files I am hoping to batch filter/align my files using biobakery workflow. When I add this trimmomatic-option to biobakery workflow I get the following error:
wmgx.py: error: unrecognized arguments: “-trimmomatic-options=LEADING:3 -trimmomatic-options=TRAILING:3 -trimmomatic-options=MINLEN:36“
Please see code below:
biobakery_workflows wmgx
–input raw_reads_test
–output test_workflow
–contaminate-databases murine_reference/mouse_C57BL_6NJ
–contaminate-databases human_reference/hg37dec_v0
–qc-options= “-trimmomatic-options=“LEADING:3” -trimmomatic-options=“TRAILING:3” -trimmomatic-options=“MINLEN:36” “
Is there another way to introduce those parameter changes in the workflow?
Thank you for your help.