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nf-core / rnavar

gatk4 RNA variant calling pipeline
https://nf-co.re/rnavar
MIT License
38 stars 32 forks source link

Warning about GATK4_HAPLOTYPECALLERGVCF #83

Open bounlu opened 1 year ago

bounlu commented 1 year ago

Description of the bug

I get the below warning:

WARN: A process with name 'GATK4_HAPLOTYPECALLERGVCF' is defined more than once in module script: /home/omeran/.nextflow/assets/nf-core/rnavar/./workflows/rnavar.nf -- Make sure to not define the same function as process

Command used and terminal output

#!/bin/bash

nextflow run nf-core/rnavar \
-latest \
-profile docker \
--genome GRCh38 \
--read_length 150 \
--fasta 's3://reference/rnaseq-genome/combined.fa' \
--gtf 's3://reference/rnaseq-genome/combined.gtf' \
--star_index 's3://reference/rnaseq-genome/STAR_100/' \
--dbsnp 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz' \
--dbsnp_tbi 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi' \
--known_indels 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz' \
--known_indels_tbi 's3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi' \
--annotate_tools merge \
--snpeff_db 'GRCh38.99' \
--vep_species 'homo_sapiens' \
--vep_genome 'GRCh38' \
--vep_cache_version \'108\' \
--max_cpus 512 \
--max_memory '2048.GB' \
--input 'samplesheet_rnaseq.csv' \
--outdir 's3://nextflow/rnavar/results/' \
-bucket-dir 's3://nextflow/rnavar/work/' \
-work-dir 's3://nextflow/rnavar/work/' \
-c 'custom.config' \
-r dev \
-resume

Relevant files

No response

System information

No response

maxulysse commented 1 year ago

Hi @bounlu thanks for reporting that, this WARNING is a known bug, but the pipeline should run its course. https://github.com/nextflow-io/nextflow/issues/3560

We'll fix that in the coming release.