Merge branch 'develop' into feature/container-engines

.github/workflows/nextflow.yaml

@@ -35,16 +35,17 @@ jobs:
         path: funnel
 
     - name: Start Funnel
-      working-directory: 
       run: |
         cd funnel/
         chmod +x ./funnel
         ./funnel server --LocalStorage.AllowedDirs $HOME run &
 
     - name: Install Nextflow
       run: |
-        curl -s https://get.nextflow.io | bash
-        chmod +x nextflow
+        cd ..
+        git clone https://github.com/nextflow-io/nextflow
+        cd nextflow
+        make compile
 
     - name: Install nf-canary and GA4GH-TES plugin
       run: |

.github/workflows/tests.yaml

@@ -17,7 +17,7 @@ jobs:
         with:
           version: latest
           # TODO: Re-enable all linters
-          args: --timeout 3m --verbose -D unused -D errcheck -D staticcheck -D govet -D gosimple
+          args: --timeout 3m --verbose -D unused -D errcheck -D staticcheck -D govet -D gosimple -D ineffassign -D typecheck
 
   build:
     runs-on: ubuntu-latest
@@ -139,4 +139,4 @@ jobs:
         make start-generic-s3
         sleep 10
         make test-generic-s3
-          
+          

go.mod

@@ -6,29 +6,29 @@ toolchain go1.22.2
 
 require (
 	cloud.google.com/go/datastore v1.17.1
-	cloud.google.com/go/pubsub v1.39.0
+	cloud.google.com/go/pubsub v1.40.0
 	github.com/Microsoft/go-winio v0.6.2 // indirect
 	github.com/Shopify/sarama v1.38.1
 	github.com/alecthomas/units v0.0.0-20231202071711-9a357b53e9c9
 	github.com/andreyvit/diff v0.0.0-20170406064948-c7f18ee00883
 	github.com/armon/circbuf v0.0.0-20190214190532-5111143e8da2
-	github.com/aws/aws-sdk-go v1.54.5
+	github.com/aws/aws-sdk-go v1.55.1
 	github.com/boltdb/bolt v1.3.1
 	github.com/cenkalti/backoff v2.2.1+incompatible
 	github.com/dgraph-io/badger/v2 v2.2007.4
 	github.com/dgryski/go-farm v0.0.0-20200201041132-a6ae2369ad13 // indirect
-	github.com/docker/docker v27.0.0+incompatible
+	github.com/docker/docker v27.1.1+incompatible
 	github.com/docker/go-connections v0.5.0 // indirect
 	github.com/docker/go-units v0.5.0 // indirect
 	github.com/elazarl/go-bindata-assetfs v1.0.1
 	github.com/gammazero/workerpool v1.1.3
-	github.com/getkin/kin-openapi v0.125.0
+	github.com/getkin/kin-openapi v0.126.0
 	github.com/getlantern/deepcopy v0.0.0-20160317154340-7f45deb8130a
 	github.com/ghodss/yaml v1.0.0
 	github.com/gizak/termui v2.3.0+incompatible
 	github.com/go-ini/ini v1.67.0 // indirect
 	github.com/go-ole/go-ole v1.3.0 // indirect
-	github.com/go-test/deep v1.1.0
+	github.com/go-test/deep v1.1.1
 	github.com/golang/gddo v0.0.0-20210115222349-20d68f94ee1f
 	github.com/golang/protobuf v1.5.4
 	github.com/grpc-ecosystem/go-grpc-middleware v1.4.0
@@ -44,38 +44,38 @@ require (
 	github.com/ncw/swift v1.0.53
 	github.com/nu7hatch/gouuid v0.0.0-20131221200532-179d4d0c4d8d
 	github.com/prometheus/client_golang v1.19.1
-	github.com/prometheus/common v0.54.0
+	github.com/prometheus/common v0.55.0
 	github.com/rs/xid v1.5.0
 	github.com/shirou/gopsutil v3.21.11+incompatible
 	github.com/sirupsen/logrus v1.9.3
 	github.com/spf13/cobra v1.8.1
 	github.com/spf13/pflag v1.0.5
 	github.com/stretchr/testify v1.9.0
-	go.mongodb.org/mongo-driver v1.15.1
-	golang.org/x/crypto v0.24.0
-	golang.org/x/net v0.26.0
+	go.mongodb.org/mongo-driver v1.16.0
+	golang.org/x/crypto v0.25.0
+	golang.org/x/net v0.27.0
 	golang.org/x/oauth2 v0.21.0
 	golang.org/x/time v0.5.0
-	google.golang.org/api v0.184.0
-	google.golang.org/genproto v0.0.0-20240604185151-ef581f913117 // indirect
-	google.golang.org/grpc v1.64.0
+	google.golang.org/api v0.186.0
+	google.golang.org/genproto v0.0.0-20240617180043-68d350f18fd4 // indirect
+	google.golang.org/grpc v1.65.0
 	gopkg.in/olivere/elastic.v5 v5.0.86
-	k8s.io/api v0.31.0-alpha.2
-	k8s.io/apimachinery v0.31.0-alpha.2
-	k8s.io/client-go v0.31.0-alpha.2
+	k8s.io/api v0.31.0-beta.0
+	k8s.io/apimachinery v0.31.0-beta.0
+	k8s.io/client-go v0.31.0-beta.0
 )
 
 require (
 	github.com/gogo/protobuf v1.3.2
 	github.com/grpc-ecosystem/grpc-gateway/v2 v2.20.0
 	github.com/hashicorp/go-multierror v1.1.1
-	google.golang.org/genproto/googleapis/api v0.0.0-20240610135401-a8a62080eff3
+	google.golang.org/genproto/googleapis/api v0.0.0-20240617180043-68d350f18fd4
 	google.golang.org/protobuf v1.34.2
 )
 
 require (
 	cloud.google.com/go v0.115.0 // indirect
-	cloud.google.com/go/auth v0.5.1 // indirect
+	cloud.google.com/go/auth v0.6.0 // indirect
 	cloud.google.com/go/auth/oauth2adapt v0.2.2 // indirect
 	cloud.google.com/go/compute/metadata v0.3.0 // indirect
 	cloud.google.com/go/iam v1.1.8 // indirect
@@ -95,7 +95,7 @@ require (
 	github.com/eapache/queue v1.1.0 // indirect
 	github.com/emicklei/go-restful/v3 v3.12.1 // indirect
 	github.com/felixge/httpsnoop v1.0.4 // indirect
-	github.com/fxamacker/cbor/v2 v2.7.0-beta // indirect
+	github.com/fxamacker/cbor/v2 v2.7.0 // indirect
 	github.com/gammazero/deque v0.2.1 // indirect
 	github.com/go-logr/logr v1.4.2 // indirect
 	github.com/go-logr/stdr v1.2.2 // indirect
@@ -111,7 +111,7 @@ require (
 	github.com/google/s2a-go v0.1.7 // indirect
 	github.com/google/uuid v1.6.0 // indirect
 	github.com/googleapis/enterprise-certificate-proxy v0.3.2 // indirect
-	github.com/googleapis/gax-go/v2 v2.12.4 // indirect
+	github.com/googleapis/gax-go/v2 v2.12.5 // indirect
 	github.com/hashicorp/errwrap v1.1.0 // indirect
 	github.com/hashicorp/go-uuid v1.0.3 // indirect
 	github.com/inconshreveable/mousetrap v1.1.0 // indirect
@@ -168,17 +168,17 @@ require (
 	go.opentelemetry.io/otel/sdk v1.27.0 // indirect
 	go.opentelemetry.io/otel/trace v1.27.0 // indirect
 	golang.org/x/sync v0.7.0 // indirect
-	golang.org/x/sys v0.21.0 // indirect
-	golang.org/x/term v0.21.0 // indirect
+	golang.org/x/sys v0.22.0 // indirect
+	golang.org/x/term v0.22.0 // indirect
 	golang.org/x/text v0.16.0 // indirect
-	google.golang.org/genproto/googleapis/rpc v0.0.0-20240604185151-ef581f913117 // indirect
+	google.golang.org/genproto/googleapis/rpc v0.0.0-20240617180043-68d350f18fd4 // indirect
 	gopkg.in/inf.v0 v0.9.1 // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect
 	gotest.tools/v3 v3.4.0 // indirect
-	k8s.io/klog/v2 v2.120.1 // indirect
-	k8s.io/kube-openapi v0.0.0-20240521193020-835d969ad83a // indirect
-	k8s.io/utils v0.0.0-20240502163921-fe8a2dddb1d0 // indirect
+	k8s.io/klog/v2 v2.130.1 // indirect
+	k8s.io/kube-openapi v0.0.0-20240430033511-f0e62f92d13f // indirect
+	k8s.io/utils v0.0.0-20240711033017-18e509b52bc8 // indirect
 	sigs.k8s.io/json v0.0.0-20221116044647-bc3834ca7abd // indirect
 	sigs.k8s.io/structured-merge-diff/v4 v4.4.1 // indirect
 	sigs.k8s.io/yaml v1.4.0 // indirect