Hello I am having the same issue as < Francesco Lescai> and nf-core #createpanelrefs

Hello, I am having the same issue as <@UT486V1V1> ...

Mira Sarkis

05/23/2025, 9:08 AM

Hello, I am having the same issue as @Francesco Lescai and @Michael Sierk with genome GATK.chr38 I tested multiple values for

igenome_base

but the bug remains

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ERROR ~ Invalid method invocation `call` with arguments: [[id:null], /ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict] (java.util.LinkedList) on _closure6 type

I even tested (with no success) using the explicit params:

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--fasta <s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta> \
  --dict  <s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict> \
  --gtf   <s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Genes/genes.gtf>

Could anyone help with this please ? Thanks in advance

Maxime Garcia

05/23/2025, 10:55 AM

I have a pull request https://github.com/nf-core/createpanelrefs/pull/50 that should solve this issue

Maxime Garcia

05/23/2025, 10:56 AM

if you want to try it, you can try:

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nextflow run maxulysse/nf-core_createpanelrefs -r mutect2_once_more ...

instead of:

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nextflow run nf-core/createpanelrefs -r dev ...

Mira Sarkis

05/23/2025, 10:57 AM

thanks for the details. I will test it now and let you know

Mira Sarkis

05/23/2025, 11:09 AM

it is working now

Mira Sarkis

05/23/2025, 11:14 AM

I updated the following issue to point to the above solution https://github.com/nf-core/createpanelrefs/issues/39, just in case someone else is testing the pipeline

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