Fix failOnIgnore causes task monitor to stop submitting tasks (#5293)

Signed-off-by: Ben Sherman <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Oct 2, 2024 · d687033 · d687033
1 parent 290f2d0
commit d687033
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Showing 5 changed files with 45 additions and 9 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -828,6 +828,12 @@ class Session implements ISession {
 
     boolean isSuccess() { !aborted && !cancelled && !failOnIgnore }
 
+    boolean canSubmitTasks() {
+        // tasks should be submitted even when 'failOnIgnore' is set to true
+        // https://github.com/nextflow-io/nextflow/issues/5291
+        return !aborted && !cancelled
+    }
+
     void processRegister(TaskProcessor process) {
         log.trace ">>> barrier register (process: ${process.name})"
         processesBarrier.register(process)

diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskPollingMonitor.groovy
@@ -587,7 +587,7 @@ class TaskPollingMonitor implements TaskMonitor {
 
         int count = 0
         def itr = pendingQueue.iterator()
-        while( itr.hasNext() && session.isSuccess() ) {
+        while( itr.hasNext() && session.canSubmitTasks() ) {
             final handler = itr.next()
             submitRateLimit?.acquire()
             try {

diff --git a/tests/checks/error-ignore-then-fail.nf/.checks b/tests/checks/error-ignore-then-fail.nf/.checks
@@ -8,5 +8,6 @@ set -e
 
 [ $status -ne 0 ] || false
 
-[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 1 ]] || false
+[[ `< .nextflow.log grep -c 'Submitted process > foo'` == 3 ]] || false
+[[ `< .nextflow.log grep -c 'Submitted process > bar'` == 1 ]] || false
 [[ `< .nextflow.log grep -c 'Error is ignored'` == 1 ]] || false
diff --git a/tests/checks/error-ignore-then-fail.nf/.config b/tests/checks/error-ignore-then-fail.nf/.config
@@ -1 +1,6 @@
-workflow.failOnIgnore = true
+workflow {
+    failOnIgnore = true
+}
+process {
+  errorStrategy = 'ignore'
+}
diff --git a/tests/error-ignore-then-fail.nf b/tests/error-ignore-then-fail.nf
@@ -15,15 +15,39 @@
  * limitations under the License.
  */
 
+workflow {
+    input_channel = channel.of("SAMP1", "SAMP2", "SAMP3")
+    foo(input_channel)
+    bar(foo.out.sample_ids.collect())
+}
+
 process foo {
-    errorStrategy 'ignore'
+    input:
+    val sample_id
+
+    output:
+    val sample_id, emit: sample_ids
 
     script:
-    '''
-    exit 1
-    '''
+    """
+    if [[ $sample_id == "SAMP1" ]]; then
+        exit 2
+    fi
+    ls -lah .*
+    """
 }
 
-workflow {
-    foo()
+process bar {
+    input:
+    val ready
+
+    output:
+    stdout
+
+    script:
+    """
+    ls -lah .*
+    """
+
 }
+