ERROR: You must provide the Tumor BAM files to the option --lbams ; Aborting.

tgen / vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files

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ERROR: You must provide the Tumor BAM files to the option --lbams ; Aborting. #13

Closed awchrist closed 5 years ago

awchrist commented 5 years ago

I am getting the following error, however there is no option "--lbams" based on the options list. ERROR: You must provide the Tumor BAM files to the option --lbams ; Aborting.

awchrist commented 5 years ago

When it fails this check it is also not exiting with a non zero exit status.

ChristopheLegendre commented 5 years ago

forgot to add the number 1 into the exit status code when an error is raised; --> FIXED
--lbams was a typo in the error message ; --bams is correct as you figured. --> FIXED
Added testing the value of the variable skip-prep-vcfs when strelka2 tool is provided; --FIXED line 844 and 846 in vcfMErger2 code version 0.7.6 ; creation of release 0.7.7