After rerunning the pipeline with ./pigx-sars-cov2-ww -s tests/settings.yaml tests/sample_sheet.csv --force --printshellcmds, which basically forces snakemake to run all rules again, the following error occurred.
WARNING: No input file format specified - detected vcf format
-------------------- EXCEPTION --------------------
MSG: ERROR: Stats file /home/agosdsc/projects/pigx/pigx_sarscov2_ww/tests/output/variants/Test0_vep_sarscov2.txt_summary.html already exists. Specify a different output file with --stats_file, overwrite existing file with --force_overwrite or disable stats with --no_stats
STACK Bio::EnsEMBL::VEP::BaseRunner::get_stats_file_handle /gnu/store/yg2a2qlj22wgk0n0r3m6xlmc1vjkdi8b-ensembl-vep-103.1/lib/perl5/site_perl/Bio/EnsEMBL/VEP/BaseRunner.pm:270
STACK Bio::EnsEMBL::VEP::Runner::init /gnu/store/yg2a2qlj22wgk0n0r3m6xlmc1vjkdi8b-ensembl-vep-103.1/lib/perl5/site_perl/Bio/EnsEMBL/VEP/Runner.pm:151
STACK Bio::EnsEMBL::VEP::Runner::run /gnu/store/yg2a2qlj22wgk0n0r3m6xlmc1vjkdi8b-ensembl-vep-103.1/lib/perl5/site_perl/Bio/EnsEMBL/VEP/Runner.pm:203
STACK toplevel /gnu/store/yg2a2qlj22wgk0n0r3m6xlmc1vjkdi8b-ensembl-vep-103.1/bin/.vep-real:232
Date (localtime) = Tue Mar 15 20:19:40 2022
Ensembl API version = 103
---------------------------------------------------
Solution would probably be to follow the advice in the error message and pass the additional --force_overwrite flag to the vep command.
After rerunning the pipeline with
./pigx-sars-cov2-ww -s tests/settings.yaml tests/sample_sheet.csv --force --printshellcmds, which basically forces snakemake to run all rules again, the following error occurred.Solution would probably be to follow the advice in the error message and pass the additional
--force_overwriteflag to the vep command.