diff --git a/nextflow.config b/nextflow.config index 3c8efce9..f5d8e226 100755 --- a/nextflow.config +++ b/nextflow.config @@ -28,6 +28,7 @@ params { clair3_docker_name = "hkubal/clair3:latest" // used for variant call deepsignal2_docker_name = "liuyangzzu/deepsignal2:v1.0" // used for deepsignal v2 guppy_stable_name = "liuyangzzu/guppy_stable:v6.3.8" // solve issues for guppy meth call in v6.4.6 + preprocessing_docker_name = "liuyangzzu/preprocessing" // for untar preprocessing // process and executor configurations executor = null @@ -268,6 +269,9 @@ profiles { container = params.docker_name containerOptions = params.containerOptions // or "--gpus all" Note: this is not compatible with GitHub citest/naive docker users + withName: 'UNTAR' { + container = params.preprocessing_docker_name + } withName: 'Tombo|DeepMod|METEORE' { container = params.tombo_docker_name } @@ -304,6 +308,10 @@ profiles { container = params.singularity_name containerOptions = params.containerOptions // "--nv" + withName: 'UNTAR' { + container = params.preprocessing_docker_name.startsWith("/") ? + params.preprocessing_docker_name : "docker://${params.tombo_docker_name}" + } withName: 'Tombo|DeepMod|METEORE' { // container = "docker://${params.tombo_docker_name}" // reserve local image for singularity, or append docker:// header for online image