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epi2me-labs / wf-metagenomics

Metagenomic classification of long-read sequencing data
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ERROR ~ Validation of pipeline parameters failed! (fastq/bam) #112

Closed LucyNanopore closed 4 months ago

LucyNanopore commented 4 months ago

Ask away!

I am trying to run the following nanopore sequencing pipeline: nextflow run epi2me-labs/wf-metagenomics \ --fastq $fastq_path \ -profile singularity \ --kraken2_memory_mapping \ --database_set PlusPF-8 \ --amr \ --amr_db resfinder \ --out_dir $output However, I get the following error message: ERROR ~ Validation of pipeline parameters failed!

-- Check '.nextflow.log' file for details ERROR ~ * Bad parameter configuration. You must select only one option of: --fastq --bam

-- Check '.nextflow.log' file for details /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 44: --fastq: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 46: -profile: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 49: --kraken2_memory_mapping: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 50: --database_set: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 53: --amr: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 54: --amr_db: command not found /opt/sge/default/spool/gpu-49/job_scripts/1783636: line 56: --out_dir: command not found

I have my barcodes in a separate folder, all of them only contain the fastq.gz files, and have been puzzled as the config file I am using has no mention of bam.

nggvs commented 4 months ago

Hi @LucyNanopore , would you mind to open this as bug completing the formular? It asks for some info that may be helpful for solving the problem :) Thank you very much in advance!

nggvs commented 4 months ago

No problem at all! When you click on new issue, you can choose between 3 models: image

Bug is for problems (it asks you for example the version of the workflow or the parameters you're using so that is more helpful to reproduce the errors), Questions are more appropriate if you want to ask something not in the docs and feature request is for feedback or things that you'd like to have in the workflow :)

Let me know if you don't find it

LucyNanopore commented 4 months ago

Thank you, I have opened one now :)