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replikation / poreCov

SARS-CoV-2 workflow for nanopore sequence data
https://case-group.github.io/
GNU General Public License v3.0
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Include artic-tools "validate_scheme" #222

Open DataSpott opened 2 years ago

DataSpott commented 2 years ago

Custom Primer bed-files can be tricky to set up the right way, so that Medaka will recognize them. In case of an error with the bed-file the medaka-process just fails and the workflow ends without error-message. "artic-tools" (as for in this docker: "nanozoo/artic:1.3.0-dev--2c5b6a9") includes a tool named "validate_scheme" that checks a bed-file for errors and gives useful information about what is wrong if any was encountered.

artic-tools_error2

artic-tools_error

If the bed-file is setup correctly it gives out a short summary: artic-tools

DataSpott commented 2 years ago

If using a custom primer.bed-file that contains an error the whole artic_ncov_wf:artic_medaka_custom_bed-process fails with error:20. Looking into the workdir, the process failed at follwoing command command (not given in process-script): Command failed:artic-tools check_vcf --summaryOut 6238aa8d4c66a472bb0a0b37.vcfreport.txt 6238aa8d4c66a472bb0a0b37.merged.vcf.gz primer_scheme/nCoV-2019/V_custom/nCoV-2019.scheme.bed 2> 6238aa8d4c66a472bb0a0b37.vcfcheck.log

6238aa8d4c66a472bb0a0b37.vcfcheck.log holds then the cause for the error of the command (here a wrong named primer-pair).