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NBISweden / pipelines-nextflow

A set of workflows written in Nextflow for Genome Annotation.
GNU General Public License v3.0
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Add fastp #4

Closed mahesh-panchal closed 4 years ago

mahesh-panchal commented 4 years ago

Change Log:

Juke34 commented 4 years ago

I don't know how to use the new options, could you update the help? https://github.com/NBISweden/pipelines-nextflow/tree/add_fastp/pipelines/TranscriptAssembly

Juke34 commented 4 years ago

does not work 

N E X T F L O W  ~  version 19.10.0
Launching `/home/jacda119/git/NBIS/pipelines-nextflow/pipelines/TranscriptAssembly/TranscriptAssembly.nf` [extravagant_lalande] - revision: 3214a0a7aa
Unknown config attribute `trimming_tools` -- check config file: /projects/test/test_nextflow/TranscriptAssembly/stranded/params.config

My parameter file contains:

params.trimmer = trimming_tools[0]
mahesh-panchal commented 4 years ago

Well, that is supposed to have a string value that you give. I'll change the code so 'fastp' is the default then, rather than the first trimmer in the list of tools.

Juke34 commented 4 years ago

Error executing process > 'transcript_assembly:multiqc'

is the path wrong? params.multiqc_config = "$baseDir/config/multiqc_conf.yml"

mahesh-panchal commented 4 years ago

The path should be correct.