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|
{ pkgs, ... }:
let
# This is the default image used by Nextflow if docker.enabled=true and no
# process.container is defined.
bash = pkgs.dockerTools.pullImage {
imageName = "quay.io/nextflow/bash";
imageDigest = "sha256:bea0e244b7c5367b2b0de687e7d28f692013aa18970941c7dd184450125163ac";
sha256 = "161s9f24njjx87qrwq0c9nmnwvyc6iblcxka7hirw78lm7i9x4w5";
finalImageName = "quay.io/nextflow/bash";
};
hello = pkgs.stdenv.mkDerivation {
name = "nextflow-hello";
src = pkgs.fetchFromGitHub {
owner = "nextflow-io";
repo = "hello";
rev = "afff16a9b45c8e8a4f5a3743780ac13a541762f8";
hash = "sha256-c8FirHc+J5Y439g0BdHxRtXVrOAzIrGEKA0m1mp9b/U=";
};
installPhase = ''
cp -r $src $out
'';
};
run-nextflow-pipeline = pkgs.writeShellApplication {
name = "run-nextflow-pipeline";
text = ''
export NXF_OFFLINE=true
for d in true false; do
for t in true false; do
rm -f nextflow.config; touch nextflow.config
echo "docker.enabled = $d" >> nextflow.config
echo "trace.enabled = $t" >> nextflow.config
echo "Testing docker=$d trace=$t"
nextflow run -ansi-log false ${hello}
echo "PASSED docker=$d trace=$t"
done
done
'';
};
in
{
name = "nextflow";
nodes.machine =
{ ... }:
{
environment.systemPackages = [
run-nextflow-pipeline
pkgs.nextflow
];
virtualisation = {
docker.enable = true;
};
};
testScript =
{ nodes, ... }:
''
start_all()
machine.wait_for_unit("docker.service")
machine.succeed("docker load < ${bash}")
machine.succeed("run-nextflow-pipeline >&2")
'';
}
|
