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BD2KGenomics / toil-lib

A common library for functions and tools used in toil-based pipelines
Apache License 2.0
4 stars 7 forks source link

Support piped commands in docker_call #80

Closed glennhickey closed 7 years ago

glennhickey commented 7 years ago

toil-vg needs to be able to run things like vg ids -s graph.vg | vg mod -X 100 > output.graph, where vg can be a docker container.

Am currently using https://github.com/cmarkello/toil-lib/commit/75c21593abb1c5856d5e4be01ef5c1018cc13104

This logic needs to get pushed up so we don't get too far out of sync. Will make a cleaned up PR shortly.

glennhickey commented 7 years ago

I see that this function is duplicated in toil. Looking at the issues, it seems that's where it should be. Will PR this update into toil instead.

jvivian commented 7 years ago

@glennhickey — Do you want to close this and open a new issue against Toil?