From 7f39e6edbd3d2e09a908d8918139ba1e778215a3 Mon Sep 17 00:00:00 2001 From: Matthew A Richardson <55555482+mr83-uw@users.noreply.github.com> Date: Mon, 21 Oct 2024 10:08:47 -0700 Subject: [PATCH] Remove invalid equals char (#5414) [ci fast] The equals character from nf-core modules/local/hicpro/dnase_mapping_stats.nf causes pipeline to crash on SGE executor. Add "=" to list of invalid chars Signed-off-by: Matthew A Richardson <55555482+mr83-uw@users.noreply.github.com> --- .../main/groovy/nextflow/executor/AbstractGridExecutor.groovy | 2 +- .../groovy/nextflow/executor/AbstractGridExecutorTest.groovy | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy b/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy index 6d6b7cc0a4..306352bbb8 100644 --- a/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/executor/AbstractGridExecutor.groovy @@ -41,7 +41,7 @@ abstract class AbstractGridExecutor extends Executor { protected Duration queueInterval - private final static List INVALID_NAME_CHARS = [ " ", "/", ":", "@", "*", "?", "\\n", "\\t", "\\r" ] + private final static List INVALID_NAME_CHARS = [ " ", "/", ":", "@", "*", "?", "\\n", "\\t", "\\r", "=" ] private Map lastQueueStatus diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy index 244f26c359..8269e89077 100644 --- a/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy +++ b/modules/nextflow/src/test/groovy/nextflow/executor/AbstractGridExecutorTest.groovy @@ -32,11 +32,11 @@ class AbstractGridExecutorTest extends Specification { def 'should remove invalid chars from name' () { given: - def task = new TaskRun(name: 'task 90 (foo:bar/baz)') + def task = new TaskRun(name: 'task 90 = (foo:bar/baz)') def exec = [:] as AbstractGridExecutor expect: - exec.getJobNameFor(task) == 'nf-task_90_(foo_bar_baz)' + exec.getJobNameFor(task) == 'nf-task_90___(foo_bar_baz)' }