From 6e231be115c31f4e29e6deab45f668ae7e75917d Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Tue, 3 Dec 2024 09:37:57 +0000 Subject: [PATCH 1/8] [release 24.11.0-edge] Update timestamp and build number Signed-off-by: Paolo Di Tommaso --- VERSION | 2 +- .../src/main/resources/META-INF/build-info.properties | 8 ++++---- .../nextflow/src/main/resources/META-INF/plugins-info.txt | 8 ++++---- nextflow | 2 +- nextflow.md5 | 2 +- nextflow.sha1 | 2 +- nextflow.sha256 | 2 +- 7 files changed, 13 insertions(+), 13 deletions(-) diff --git a/VERSION b/VERSION index 21651351e2..2b70d664e4 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -24.10.0 +24.11.0-edge diff --git a/modules/nextflow/src/main/resources/META-INF/build-info.properties b/modules/nextflow/src/main/resources/META-INF/build-info.properties index d6072256a9..2053248f03 100644 --- a/modules/nextflow/src/main/resources/META-INF/build-info.properties +++ b/modules/nextflow/src/main/resources/META-INF/build-info.properties @@ -1,4 +1,4 @@ -build=5928 -version=24.10.0 -timestamp=1730054192154 -commitId=6524d8dc9 +build=5929 +version=24.11.0-edge +timestamp=1733218258400 +commitId=7e2c8d82b diff --git a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt index 39d506b59d..c650c71066 100644 --- a/modules/nextflow/src/main/resources/META-INF/plugins-info.txt +++ b/modules/nextflow/src/main/resources/META-INF/plugins-info.txt @@ -1,8 +1,8 @@ -nf-amazon@2.9.0 -nf-azure@1.10.1 +nf-amazon@2.10.0 +nf-azure@1.11.0 nf-cloudcache@0.4.2 nf-codecommit@0.2.2 nf-console@1.1.4 -nf-google@1.15.2 +nf-google@1.16.0 nf-tower@1.9.3 -nf-wave@1.7.2 \ No newline at end of file +nf-wave@1.8.0 \ No newline at end of file diff --git a/nextflow b/nextflow index 5dbb589bdf..c89ca7617d 100755 --- a/nextflow +++ b/nextflow @@ -15,7 +15,7 @@ # limitations under the License. [[ "$NXF_DEBUG" == 'x' ]] && set -x -NXF_VER=${NXF_VER:-'24.10.0'} +NXF_VER=${NXF_VER:-'24.11.0-edge'} NXF_ORG=${NXF_ORG:-'nextflow-io'} NXF_HOME=${NXF_HOME:-$HOME/.nextflow} NXF_PROT=${NXF_PROT:-'https'} diff --git a/nextflow.md5 b/nextflow.md5 index c51c7ce709..deb7f7a40a 100644 --- a/nextflow.md5 +++ b/nextflow.md5 @@ -1 +1 @@ -7dfd8066370310bff610aa209c988b3e +66995c4139ebcd17bf99f17d9dd030d1 diff --git a/nextflow.sha1 b/nextflow.sha1 index 80cc138bfd..ccadbdc25f 100644 --- a/nextflow.sha1 +++ b/nextflow.sha1 @@ -1 +1 @@ -c142828a82fa6678a5af978d3545bb7f56072be6 +cdbb67bdb21c0e63fb48aabb8b168c12a31fa5b3 diff --git a/nextflow.sha256 b/nextflow.sha256 index e9a09bcc10..f4e9ccb3bd 100644 --- a/nextflow.sha256 +++ b/nextflow.sha256 @@ -1 +1 @@ -e848918fb9b85762822c078435d9ff71979a88cccff81ce5babd75d5eee52fe6 +69a86852c52dcfa7662407c46d16f05bd3dec16e0c505c2a2f71ccc56219d631 From 51aea8f389adbaff8e820d226337c47587ad3c57 Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Tue, 3 Dec 2024 10:46:44 +0000 Subject: [PATCH 2/8] Update changelog [ci skip] Signed-off-by: Paolo Di Tommaso --- changelog.txt | 41 +++++++++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) diff --git a/changelog.txt b/changelog.txt index 0be1d17adf..54fba39ad4 100644 --- a/changelog.txt +++ b/changelog.txt @@ -1,5 +1,46 @@ NEXTFLOW CHANGE-LOG =================== +24.11.0-edge - 3 Dec 2024 +- Add GHA to submit dependencies to dependabot (#5440) [80395a6d] +- Add NotFoundException to retry condition for Google Batch [aa4d19cc] +- Add Rahel Hirsch to run name generator (#5442) [ff2bc6ae] +- Add `env()` function (#5506) [fa0e8e0f] +- Add more scientists to run name generator (#5447) [38d9eda0] +- Add `singularity.libraryDir` to config page (#5498) [b5e31bb0] +- Add RepositoryProvider.revision now public property (#5500) [f0a4c526] +- Deprecate process `shell` block (#5508) [6f527551] +- Detecting errors in data unstaging (#5345) [3c8e602d] +- Disable virtual threads on CI tests [ci slip] [69d07dbc] +- Fix Fargate warning on memory check (#5475) [bdf0ad00] +- Fix `isContainerReady` when wave is disabled (#5509) [3215afa8] +- Fix missing wave response (#5547) [ee252173] +- Fix overlapping conda lock file (#5540) [9248c04d] +- Fix overlapping conda lock exception (#5489) [eaaeb3de] +- Fix possible deadlock in dynamic `maxRetry` resolution (#5474) [25bbb621] +- Fix Wave GCP integration test (#5490) [ad56c89b] +- Fixing bug when execution with stub and no stub defined (#5473) [f7fd56db] +- Fix Incorrect CPU value in Azure example (#5549) [fc5e2c2a] +- Improve docs for using the GPU accelerator directive (#5488) [4b908524] +- Improve groupTuple docs with scatter/gather example (#5520) [b5c63a9f] +- Prevent NPE with null AWS Batch response [12fc1d60] +- Target Java 17 as minimal Java version (#5045) [0140f954] +- Update 'nexus-staging' plugin to latest version (#5462) [07934513] +- Update gradle 'shadow' plugin version to 8.3.5 (#5463) [2a5f15f0] +- Update install docs to reflect change from 'all' to 'dist' (#5496) [c9115659] +- Update process snippets to comply with strict syntax (#5526) [be1694bf] +- Update Wave dependencies [09ccd295] +- Bump aws sdk 1.12.777 (#5458) [8bad0b4b] +- Bump bouncycastle to jdk18on:1.78.1 (#5467) [cd8c385f] +- Bump com.azure:azure-identity from 1.11.3 to 1.12.2 (#5449) [cb70f1df] +- Bump commons-io:2.15.1 [767e4a0a] +- Bump groovy 4.0.24 [dd71ad31] +- Bump netty-common to version 4.1.115.Final [d1bbd3d0] +- Bump nf-amazon@2.10.0 [2b653b07] +- Bump nf-azure@1.11.0 [6af7198d] +- Bump nf-google@1.16.0 [9494f970] +- Bump nf-google@1.8.0 [7e2c8d82] +- Bump protobuf-java:3.25.5 to nf-google [488b7906] + 24.10.2 - 27 Nov 2024 - Prevent NPE with null AWS Batch response [3d491934] - Fix overlapping conda lock file (#5540) [df66deaa] From 12be47efa0cce264e0a8d82eb4f4bdcdb837362a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 4 Dec 2024 11:11:06 +0100 Subject: [PATCH 3/8] Improve Fargate + Wave docs (#5562) [ci skip] Signed-off-by: Phil Ewels Signed-off-by: Paolo Di Tommaso Co-authored-by: Paolo Di Tommaso Co-authored-by: Christopher Hakkaart --- docs/aws.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/aws.md b/docs/aws.md index ba518ad7ae..84ab5c448f 100644 --- a/docs/aws.md +++ b/docs/aws.md @@ -539,7 +539,8 @@ See the AWS documentation for details how to create the required AWS Batch queue and the Batch Execution Role. :::{note} -This feature requires the use {ref}`Wave ` container provisioning service. +Nextflow uses [s5cmd](https://github.com/peak/s5cmd) to download the task input data and upload the task outputs. +To enable this capability, you need to enable the Wave service in the Nextflow configuration, as shown in the above example. See {ref}Wave documentation for more details. ::: ## Advanced configuration From 54713a16a006161f453f3215440253e57b08064d Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 4 Dec 2024 11:12:52 +0100 Subject: [PATCH 4/8] Customise mermaid diagram theme in DAG template (#5553) [ci skip] Signed-off-by: Phil Ewels --- docs/_static/dag.mmd | 14 ++++++++++++++ .../nextflow/dag/mermaid.dag.template.html | 14 ++++++++++++++ 2 files changed, 28 insertions(+) diff --git a/docs/_static/dag.mmd b/docs/_static/dag.mmd index 0963e2c106..989a536ae9 100644 --- a/docs/_static/dag.mmd +++ b/docs/_static/dag.mmd @@ -1,3 +1,17 @@ +%%{ + init: { + 'theme': 'base', + 'themeVariables': { + 'primaryColor': '#B6ECE2', + 'primaryTextColor': '#160F26', + 'primaryBorderColor': '#065647', + 'lineColor': '#545555', + 'clusterBkg': '#BABCBD22', + 'clusterBorder': '#DDDEDE', + 'fontFamily': 'arial' + } + } +}%% flowchart TB subgraph " " v0["Channel.fromFilePairs"] diff --git a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html index 47062c1218..0ab1d9475e 100644 --- a/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html +++ b/modules/nextflow/src/main/resources/nextflow/dag/mermaid.dag.template.html @@ -19,6 +19,20 @@ 
+%%{
+  init: {
+    'theme': 'base',
+    'themeVariables': {
+      'primaryColor': '#B6ECE2',
+      'primaryTextColor': '#160F26',
+      'primaryBorderColor': '#065647',
+      'lineColor': '#545555',
+      'clusterBkg': '#BABCBD22',
+      'clusterBorder': '#DDDEDE',
+      'fontFamily': 'arial'
+    }
+  }
+}%%
 REPLACE_WITH_NETWORK_DATA