Fixes crash when performing variant annotation without filtering. - #9
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FreekManders wants to merge 1 commit into
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Fixes crash when performing variant annotation without filtering.#9FreekManders wants to merge 1 commit into
FreekManders wants to merge 1 commit into
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…s crash is caused by the gatk_variantfiltration.out variable not being created when filtering is not performed.
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Hi Freek, I do agree that this solves this particular issue for now. A similar error will still occur when you start the workflow from fastq/bam , do germlineCalling BUT skip variantFiltration. In general I have to find a way to work around checking on channel.out , since that doesn't seem to work the way I want it to. |
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When variant annotation is performed without filtering the pipeline crashes. This crash is caused by the
gatk_variantfiltration.outvariable not being created when filtering is not performed.I'm not familiar with nextflow so I just added an extra if statement around this variable to prevent the issue. This does make my fix rather ugly though. A check to see if the variable exists might be prettier.