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Clinical-Genomics / raredisease

CG's rare disease pipeline in next flow, see the main repo here 👇
https://github.com/nf-core/raredisease
MIT License
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Config file fails with error when submitting job through cg run. #18

Closed peterpru closed 6 months ago

peterpru commented 6 months ago

Description of the bug

When launching the raredisease pipeline using cg workflow raredisease run CASE, the job terminates in nf-tower with the following error:

`N E X T F L O W  ~  version 23.10.1
Pulling nf-core/raredisease ...
downloaded from https://github.com/nf-core/raredisease.git
Launching `https://github.com/nf-core/raredisease` [funkitten_from3Sq6wUrlUn0yur_20240321091934] DSL2 - revision: c371602095 [1.1.1]
WARN: Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: 'NXF_SINGULARITY_CACHEDIR'
WARN: The following invalid input values have been detected:
* --cnvnator_binsize: 1000
* --gens_pon_female: /home/proj/stage/workflows/raredisease/references/references_dev//grch37_gens_female_pon_100bp.hdf5
* --gens_pon_male: /home/proj/stage/workflows/raredisease/references/references_dev//grch37_gens_male_pon_100bp.hdf5
* --mobile_element_references: /home/proj/stage/workflows/raredisease/references/references_dev//grch37_mobile_element_references.tsv
* --mobile_element_svdb_annotations: /home/proj/stage/workflows/raredisease/references/references_dev//grch37_mobile_element_svdb_annotations.csv
* --score_config_mt: /home/proj/stage/workflows/raredisease/references/references_dev//rank_model_-v1.35-.ini
* --skip_gens: false
* --skip_germlinecnvcaller: true
* --skip_vcf2cytosure: false
* --svdb_query_bedpedbs: /home/proj/stage/workflows/raredisease/references/references_dev//svdb_query_bedpedbs.csv
* --variant_consequences_snv: /home/proj/stage/workflows/raredisease/references/references_dev//variant_consequences_snv_v0.txt
* --variant_consequences_sv: /home/proj/stage/workflows/raredisease/references/references_dev//variant_consequences_sv_v0.txt
* --vep_plugin_files: /home/proj/stage/workflows/raredisease/references/references_dev//vep_files.csv
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check 'nf-5Vm36UustQQUz0.log' file for details
The following invalid input values have been detected:
* --vep_cache_version: '110' is not a valid choice (Available choices: 107)
-- Check script '/home/proj/stage/analysis/cases/funkitten/work/.nextflow/pipelines/24177de6/nf-core/raredisease/main.nf' at line: 73 or see 'nf-5Vm36UustQQUz0.log' file for more details`

Command used and terminal output

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Relevant files

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System information

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jemten commented 6 months ago

Could you try to update the config to launch version 2.0.0? I believe that the configs were written for the dev branch which should now resemble the latest release.

peterpru commented 6 months ago

Tested with 2.0.1, new errors on gens. Working on it now.


N E X T F L O W  ~  version 23.10.1
Pulling nf-core/raredisease ...
downloaded from https://github.com/nf-core/raredisease.git
Launching `https://github.com/nf-core/raredisease` [justhusky] DSL2 - revision: 1489b71cc0 [2.0.1]
WARN: Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: 'NXF_SINGULARITY_CACHEDIR'
WARN: Nextflow variables must be defined in the launching environment - The following variable set in the config file is going to be ignored: 'NXF_DISABLE_CHECK_LATEST'
params.gens_gnomad_pos not set.
params.gens_interval_list not set.
params.gens_pon_female not set.
params.gens_pon_male not set.
Set missing parameters and restart the run. For more information please check usage documentation on github.
peterpru commented 6 months ago

Fixed by https://github.com/Clinical-Genomics/servers/pull/1323. Closing as completed.