revert to old config for pytests

nf-core · Dec 13, 2024 · 0433a66 · 0433a66
1 parent 381118f
commit 0433a66
Showing 1 changed file with 19 additions and 58 deletions.
diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config
@@ -13,64 +13,25 @@ process {
     ]
 }
 
-profiles {
-    conda {
-        conda.enabled           = true
-        conda.channels          = ['conda-forge', 'bioconda']
-        apptainer.enabled       = false
-    }
-    mamba {
-        conda.enabled           = true
-        conda.useMamba          = true
-    }
-    docker {
-        docker.enabled          = true
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
-    }
-    docker_self_hosted {
-        docker.enabled          = true
-        docker.userEmulation    = false
-        docker.fixOwnership     = true
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
-    }
-    arm {
-        docker.runOptions       = '-u $(id -u):$(id -g) --platform=linux/amd64'
-    }
-    singularity {
-        singularity.enabled     = true
-        singularity.autoMounts  = true
-    }
-    podman {
-        podman.enabled          = true
-        podman.runOptions       = "--runtime crun --platform linux/x86_64 --systemd=always"
-    }
-    shifter {
-        shifter.enabled         = true
-    }
-    charliecloud {
-        charliecloud.enabled    = true
-    }
-    apptainer {
-        apptainer.enabled       = true
-        apptainer.autoMounts    = true
-    }
-    wave {
-        apptainer.ociAutoPull   = true
-        singularity.ociAutoPull = true
-        wave.enabled            = true
-        wave.freeze             = true
-        wave.strategy           = 'conda,container'
-    }
-    gitpod {
-        executor.name           = 'local'
-        executor.cpus           = 4
-        executor.memory         = 8.GB
-    }
-    gpu {
-        docker.runOptions       = '-u $(id -u):$(id -g) --gpus all'
-        apptainer.runOptions    = '--nv'
-        singularity.runOptions  = '--nv'
-    }
+if ("$PROFILE" == "singularity") {
+    singularity.enabled = true
+    singularity.autoMounts = true
+} else if ("$PROFILE" == "conda") {
+    conda.enabled = true
+    conda.useMicromamba = true
+} else if ("$PROFILE" == "mamba") {
+    conda.enabled  = true
+    conda.useMamba = true
+    conda.useMicromamba = true
+} else if ("$PROFILE" == "podman") {
+    podman.enabled = true
+    podman.userEmulation = true
+    podman.runOptions = "--runtime crun --platform linux/x86_64 --systemd=always"
+} else {
+    docker.enabled = true
+    docker.userEmulation = false
+    docker.fixOwnership = true
+    docker.runOptions = '--platform=linux/amd64'
 }
 
 docker.registry      = 'quay.io'