Validation of pipeline parameters failed! #2050
Description
Description of the bug
N E X T F L O W ~ version 25.10.0
Sarek revision: 3.6.0
The following invalid input values have been detected:
* --spliceai_snv (/mnt/scratch/anita/sarek_data/annotation/spliceAI/spliceai_scores_raw_snv_hg38.vcf.gz): "/mnt/scratch/anita/sarek_data/annotation/spliceAI/spliceai_scores_raw_snv_hg38.vcf.gz" does not match regular expression [^\S+\.\vcf\.gz$]
* --dbnsfp_tbi (/home/anita/dbNSFP5.3a_grch38.gz.tbi): "/home/anita/dbNSFP5.3a_grch38.gz.tbi" does not match regular expression [^\S+\.vcf\.gz\.(csi|tbi)$]
* --spliceai_snv_tbi (/mnt/scratch/anita/sarek_data/annotation/spliceAI/spliceai_scores_raw_snv_hg38.vcf.gz.tbi): "/mnt/scratch/anita/sarek_data/annotation/spliceAI/spliceai_scores_raw_snv_hg38.vcf.gz.tbi" does not match regular expression [^\S+\\.vcf\.gz.(csi|tbi)$]
The expected regular expression is incorrect ( expecting sample.\vcf.gz for spliceai_snv and a vcf file for the dbnsfp file name)
I changed the regex in /root/.nextflow/assets/nf-core/sarek/nextflow_schema.json " and then could run the pipeline.
"dbnsfp_tbi": from "pattern": "^\\S+\\.vcf\\.gz\\.(csi|tbi)$" to "pattern": "^\\S+\\.gz\\.(csi|tbi)$"
"spliceai_snv": from "pattern": "^\\S+\\.\\vcf\\.gz$"` to "pattern": "^\\S+\\.vcf\\.gz$"
Thank you for your work.
Best,
Anita
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