Help me 🦆 s I am trying to understand why fastquorum doesn't seem to have igenomes working at the moment. When I try

nextflow run main.nf \
--input <https://raw.githubusercontent.com/nf-core/test-datasets/fastquorum/testdata/samplesheets/samplesheet.tiny.csv> \
--genome GRCh38 \
--outdir test \
-profile docker

It won't align anything. It seems to have all the required boilerplate in https://github.com/nf-core/fastquorum/blob/da1148fed20864d5e041d3201560fde74705bcb3/main.nf#L33

params.fasta     = getGenomeAttribute('fasta')
params.fasta_fai = getGenomeAttribute('fasta_fai')
params.dict      = getGenomeAttribute('dict')
params.bwa       = getGenomeAttribute('bwa')

// Initialize fasta file with meta map:
fasta = params.fasta ? Channel.fromPath(params.fasta).map{ it -> [ [id:it.baseName], it ] }.collect() : Channel.empty()

and when I try with some

println

action

getGenomeAttribute

seems to be working absolutely fine. But setting params.fasta just doesn't do anything:

params.fasta = getGenomeAttribute('fasta')
println params.fasta

gives

null

, but

params.fasta2 = getGenomeAttribute('fasta')
println params.fasta2

gives

<s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa>

What is silently stopping

params.fasta

from being reassigned here? It seems to stop the other

fasta_fai

,

dict

and

bwa

parameters on the next lines too.

I think you're hitting the issue we found out with @Ram about using the

getGenomeAtribute

function coming from a Nextflow script instead of the groovy lib

Yeah, looks the same issue

You have to move the

getGenomeAttribute

code to before you include all other subworkflows/functions 😛

It works if I remove them from being set to null in the nextflow.config

you should not set them to null in nextflow.config

even being defined after the include statements

Awesome 😛

still getting the

Access to undefined parameter

though

Do you have a PR or repo?

yeah, just give me a minute

have you added all parameters to the JSON schema?

I haven't edited the schema, but presumably they were there before?

Can you tell me what parameter is undefined? 😛

fasta, fasta_fai, dict, bwa

Can you check Sarek dev

I've tried some things but I can't seem to stop the warnings 😕

The warnings are coming from this block of code:

// Check input path parameters to see if they exist
    def checkPathParamList = [
        params.bwa,
        params.dict,
        params.fasta,
        params.fasta_fai

    ]

Is this bit of code outdated now? I can't find

checkPathParamList

used anywhere, and I can't see it in a few other pipelines.

Ah yes you can now add the

exists: true

keyword in your schema to check those parameters

Does that mean the

checkPathParamList

can be removed from sarek too?

Yes! Just make sure you add

exists

to the schema 🙂

exists

in the schema checks that the file exists if it is present?

Correct!

Great, thanks Nicolas