No such property: inittag for class: Script_c812b1e6

[pichauma]

Hi,

I have set up a new pipeline that works locally but was never run on AWS.
When running the pipeline via the curl command or the launchpad, I get the following error "No such property: inittag for class: Script_c812b1e6".

The log file is empty.
Workflow unique id: 18AFh9rlXj8XZ4
Nextflow session id is: 5d8e8239-b207-47e4-848c-8c402c462b92

Let me know what I can provide to help.
Thanks!

[pichauma]

Attached are some files to reproduce the issue.
nextflow_test1.zip

Arguments are:

• query: a folder that contains sequences
• seqname_suffix: the suffix of the sequences files, e.g. ".fq.gz"
• hostbwaindex: the folde/bwa prefix of bwa index files, e.g. "s3://[your_folder]/hg19"
• output_dir: the output folder

Running this in tower failed with:
"No such property: inittag for class: Script_90a1a932"

---

Now that I think of it ... could it be that all the arguments need to be provided values, and that the mechanism I used to provide default value fails to work in tower (see the main.nf file)?

[pichauma]

I am quite sure this is where the problem comes from.
Running the program locally, I get warnings:

Launching `main.nf` [peaceful_babbage] - revision: 05addb6a73
WARN: Access to undefined parameter `seqname_prefix` -- Initialise it to a default value eg. `params.seqname_prefix = some_value`
WARN: Access to undefined parameter `seqname_middle` -- Initialise it to a default value eg. `params.seqname_middle = some_value`
WARN: Access to undefined parameter `apiKey` -- Initialise it to a default value eg. `params.apiKey = some_value`
WARN: Access to undefined parameter `resultrepo` -- Initialise it to a default value eg. `params.resultrepo = some_value`
WARN: Access to undefined parameter `reflength_file` -- Initialise it to a default value eg. `params.reflength_file = some_value`

WARN: Access to undefined parameter `normalisation` -- Initialise it to a default value eg. `params.normalisation = some_value`

Processing QC-related arguments ...
WARN: Access to undefined parameter `fastp_arguments` -- Initialise it to a default value eg. `params.fastp_arguments = some_value`
WARN: Access to undefined parameter `host_mapfilter_arguments` -- Initialise it to a default value eg. `params.host_mapfilter_arguments = some_value`
Processing reference mapping arguments ...
WARN: Access to undefined parameter `refbwaindex` -- Initialise it to a default value eg. `params.refbwaindex = some_value`
WARN: Access to undefined parameter `ref_mapfilter_arguments` -- Initialise it to a default value eg. `params.ref_mapfilter_arguments = some_value`
done.
executor >  local (2)
[4d/96d991] process > qc_step1 (A) [100%] 2 of 2 ✔

But through tower, it crashes.
It makes me wonder how launchpad handles optional arguments.

[pichauma]

In the end, the problem was on my end.
Sorry for the bother.