Below lines of code/script will fail when doing aggregate from path, and have samples haven't finished corresponding subworkflows.
The goal of aggregate from path is to leverage whatever have already completed samples/subworkflows to construct a cohort to the best of it can. It was designed to tolerate missing samples/subworkflows and aggregate whatever there is.
Since below scripts specifically naming files, instead of using wildcard like the examples at the end here shows, the process will fail since aggrgate will create invalid link based on the path, which will be ignored by using wildcard but error will raise when specifying file names.
Below lines of code/script will fail when doing aggregate from path, and have samples haven't finished corresponding subworkflows. The goal of aggregate from path is to leverage whatever have already completed samples/subworkflows to construct a cohort to the best of it can. It was designed to tolerate missing samples/subworkflows and aggregate whatever there is. Since below scripts specifically naming files, instead of using wildcard like the examples at the end here shows, the process will fail since aggrgate will create invalid link based on the path, which will be ignored by using wildcard but error will raise when specifying file names.
https://github.com/mskcc/tempo/blob/e29f5bed924bb055f33bc0dc10a8a7319df18096/modules/process/Aggregate/GermlineAggregateSv.nf#L14 https://github.com/mskcc/tempo/blob/e29f5bed924bb055f33bc0dc10a8a7319df18096/modules/process/Aggregate/SomaticAggregateHRDetect.nf#L13 https://github.com/mskcc/tempo/blob/e29f5bed924bb055f33bc0dc10a8a7319df18096/modules/process/Aggregate/SomaticAggregateSv.nf#L14
And for loops in the script block of this process https://github.com/mskcc/tempo/blob/develop/modules/process/Aggregate/CohortRunMultiQC.nf
Successful examples: https://github.com/mskcc/tempo/blob/e29f5bed924bb055f33bc0dc10a8a7319df18096/modules/process/Aggregate/SomaticAggregateMaf.nf#L21 https://github.com/mskcc/tempo/blob/e29f5bed924bb055f33bc0dc10a8a7319df18096/modules/process/Aggregate/SomaticAggregateLOHHLA.nf#L20