Nextflow stdout:

WARN: No DADA2 cutoffs were specified (`--trunclenf` & `--trunclenr`), therefore reads will be truncated where median quality drops below 25 (defined by `--trunc_qmin`) but at least a fraction of 0.75 (defined by `--trunc_rmin`) of the reads will be retained.
The chosen cutoffs do not account for required overlap for merging, therefore DADA2 might have poor merging efficiency or even fail.

WARN: A process with name 'ANCOMBC_FORMULA_ASV' is defined more than once in module script: /home/runner/work/ampliseq/ampliseq/./workflows/../subworkflows/local/qiime2_ancom.nf -- Make sure to not define the same function as process
WARN: A process with name 'ANCOMBC_FORMULA_TAX' is defined more than once in module script: /home/runner/work/ampliseq/ampliseq/./workflows/../subworkflows/local/qiime2_ancom.nf -- Make sure to not define the same function as process
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
WARN: The following invalid input values have been detected:

* --baseDir: /home/runner/work/ampliseq/ampliseq
* --base-dir: /home/runner/work/ampliseq/ampliseq
* --outputDir: /home/runner/work/ampliseq/ampliseq/.nf-test/tests/426c81daeb6712e33b8769dc2ab56325/output
* --output-dir: /home/runner/work/ampliseq/ampliseq/.nf-test/tests/426c81daeb6712e33b8769dc2ab56325/output


ERROR ~ Unexpected error [EOFException]

 -- Check script './workflows/ampliseq.nf' at line: 322 or see '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/426c81daeb6712e33b8769dc2ab56325/meta/nextflow.log' file for more details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/426c81daeb6712e33b8769dc2ab56325/meta/nextflow.log' file for details
ERROR ~ Cannot invoke method getAt() on null object

 -- Check script './workflows/../subworkflows/local/dada2_preprocessing.nf' at line: 61 or see '/home/runner/work/ampliseq/ampliseq/.nf-test/tests/426c81daeb6712e33b8769dc2ab56325/meta/nextflow.log' file for more details
Nextflow stderr: