From 779388f871c2fe7aaddcbfe0d4ba21fd87a56654 Mon Sep 17 00:00:00 2001 From: Natalia Garcia Date: Tue, 19 May 2026 14:03:13 +0000 Subject: [PATCH] Pin wf-template@ruo-next --- .gitlab-ci.yml | 2 +- lib/common.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 82eaf6c..db34764 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -16,7 +16,7 @@ variables: PYTEST_TESTS_PATH: "bin/workflow_glue/tests/common" RTEST_CONTAINER_NAME: "wf-transcriptomes-core" RTEST_CONTAINER_CONFIG_KEY: "container_sha" - WF_TEMPLATE_ENFORCEMENT_BRANCH: "CW-6552" + WF_TEMPLATE_ENFORCEMENT_BRANCH: "ruo-next" pytest_wfcontainer: extends: pytest diff --git a/lib/common.nf b/lib/common.nf index db6055c..ac739c6 100644 --- a/lib/common.nf +++ b/lib/common.nf @@ -81,7 +81,7 @@ process minimap2_alignment { emit: alignment script: String reset_cmd_body = "samtools reset -x tp,cm,s1,s2,NM,MD,AS,SA,ms,nn,ts,cg,cs,dv,de,rl" - String fastq_cmd_body = "samtools fastq -T *" + String fastq_cmd_body = "samtools fastq -T '*'" // Default required threads is 6 // Samtools x3 and bamstats will all be single threaded def minimap2_threads = Math.max(task.cpus - 4 , 1)