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SnpEff and VEP publishDir contains a variable with a null value #125

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nschcolnicov opened this issue Feb 8, 2024 · 1 comment
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@nschcolnicov
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nschcolnicov commented Feb 8, 2024

Description of the bug

When running the pipeline using the annotate_tools SnpEff and VEP I get the error:
publishDir path contains a variable with a null value

image image

Command used and terminal output

nextflow run ../../main.nf -profile bi,cluster --input ../input.csv --genome GRCh38 --outdir . -c ../config.config --annotate_tools vep -resume --vep_cache 's3://annotation-cache/vep_cache/110_GRCh38/'

Relevant files

The config file contains all the definitions for the reference files, the vep_cache had to be specified manually because the automatic process for building its path is not currently working and is being addressed here: #106

System information

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@nschcolnicov nschcolnicov added the bug Something isn't working label Feb 8, 2024
@nschcolnicov
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This was fixed, closing this issue

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