From 12be47efa0cce264e0a8d82eb4f4bdcdb837362a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 4 Dec 2024 11:11:06 +0100 Subject: [PATCH 1/5] 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 2/5] 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'
+    }
+  }
+}%%
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