From 9efca35a5ebe2b70635482b76d169409714aaefa Mon Sep 17 00:00:00 2001 From: "Clark, Lindsay" Date: Wed, 20 May 2026 08:38:48 -0700 Subject: [PATCH 1/4] Update nf version and fix conda channel_priority command --- docs/seattlechildrens.md | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/docs/seattlechildrens.md b/docs/seattlechildrens.md index 8ea085a48..4b6d72249 100644 --- a/docs/seattlechildrens.md +++ b/docs/seattlechildrens.md @@ -29,8 +29,7 @@ channels: - conda-forge dependencies: - python>=3.9 - - nextflow==25.04.8 - - nf-core==3.4.1 + - nextflow==26.04.1 - graphviz ``` @@ -40,9 +39,9 @@ Make sure that channel priority is set to flexible using the following comments: ```bash # print your current conda settings -mamba config --describe channel_priority +conda config --describe channel_priority # set to flexible if not already done -mamba config --set channel_priority flexible +conda config --set channel_priority flexible ``` 3. Create the _Nextflow_ `mamba` environment From ef7e327bf6320b5ba93766854ece47e1e6c89799 Mon Sep 17 00:00:00 2001 From: "Clark, Lindsay" Date: Tue, 16 Jun 2026 10:00:53 -0700 Subject: [PATCH 2/4] Update time syntax --- conf/seattlechildrens.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/seattlechildrens.config b/conf/seattlechildrens.config index e45de4014..bc5b7b00d 100644 --- a/conf/seattlechildrens.config +++ b/conf/seattlechildrens.config @@ -9,7 +9,7 @@ process { executor = 'slurm' queue = 'cpu-core' memory = 7500.MB - time = '72h' + time = {System.getenv("ASSOC") == 'core' ? 4.h : 72.h} clusterOptions = "--account ${System.getenv("ASSOC")}" withLabel:'process_gpu' { From 84f2bd259649abf0ea7a9af380722df13aee414b Mon Sep 17 00:00:00 2001 From: "Clark, Lindsay" Date: Tue, 16 Jun 2026 11:34:24 -0700 Subject: [PATCH 3/4] Update Nextflow version again --- docs/seattlechildrens.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/seattlechildrens.md b/docs/seattlechildrens.md index 4b6d72249..103246b1c 100644 --- a/docs/seattlechildrens.md +++ b/docs/seattlechildrens.md @@ -29,7 +29,7 @@ channels: - conda-forge dependencies: - python>=3.9 - - nextflow==26.04.1 + - nextflow==26.04.3 - graphviz ``` From 2fa3acf8fc88007eaf4f24e7cf03b50a9315b0b4 Mon Sep 17 00:00:00 2001 From: "Clark, Lindsay" Date: Tue, 16 Jun 2026 11:44:10 -0700 Subject: [PATCH 4/4] Simplify time specification since docs assume non-core association --- conf/seattlechildrens.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/seattlechildrens.config b/conf/seattlechildrens.config index bc5b7b00d..2492158f6 100644 --- a/conf/seattlechildrens.config +++ b/conf/seattlechildrens.config @@ -9,7 +9,7 @@ process { executor = 'slurm' queue = 'cpu-core' memory = 7500.MB - time = {System.getenv("ASSOC") == 'core' ? 4.h : 72.h} + time = 72.h clusterOptions = "--account ${System.getenv("ASSOC")}" withLabel:'process_gpu' {