Remove square brackets from job name in LSF executor (#4799) [ci fast]

Signed-off-by: Brian Fulton-Howard <fultonh1@gmail.com>
Signed-off-by: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Co-authored-by: Brian Fulton-Howard <brian.fulton-howard@mssm.edu>
Co-authored-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>

modules/nextflow/src/main/groovy/nextflow/executor/LsfExecutor.groovy

@@ -112,6 +112,13 @@ class LsfExecutor extends AbstractGridExecutor {
         return result
     }
 
+    @Override
+    String sanitizeJobName( String name ) {
+        // LSF does not allow square brackets in job names except for job arrays
+        name = name.replace('[','').replace(']','')
+        // Old LSF versions do not allow job names longer than 511 chars
+        name.size()>511 ? name.substring(0,511) : name
+    }
 
     /**
      * The command line to submit this job

modules/nextflow/src/test/groovy/nextflow/executor/LsfExecutorTest.groovy

@@ -25,6 +25,8 @@ import nextflow.processor.TaskConfig
 import nextflow.processor.TaskProcessor
 import nextflow.processor.TaskRun
 import spock.lang.Specification
+import spock.lang.Unroll
+
 /**
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@@ -699,4 +701,25 @@ class LsfExecutorTest extends Specification {
         config.RESOURCE_RESERVE_PER_TASK == 'Y'
     }
 
+    // Adapted from PbsExecutorTest.groovy
+    @Unroll
+    def 'should return valid job name given #name'() {
+        given:
+        def executor = [:] as LsfExecutor
+        def task = Mock(TaskRun)
+        task.getName() >> name
+
+        expect:
+        executor.getJobNameFor(task) == expected
+        executor.getJobNameFor(task).size() <= 4094
+
+        where:
+        name               | expected
+        'hello'            | 'nf-hello'
+        '12 45'            | 'nf-12_45'
+        'hello[123]-[xyz]' | 'nf-hello123-xyz'
+        'a'.repeat(509)    | 'nf-'.concat("a".repeat(508))
+    }
+
 }
+