Calling groupTuple triggers java.lang.NullPointerException

[scwatts]

Bug report

Under certain conditions calling groupTuple appears to trigger a null pointer exception. A MRE is linked below. The process to trigger the null pointer exception in this MRE can be summarised as:

• run process ONE and TWO
• create a new channel named ch_three_input from ONE and TWO outputs
• run process THREE with input from ch_three_input
• take process THREE output and combine with ch_three_input using groupTuple

The final step that involves the groupTuple call triggers the exception. I don't think I'm using channels in an unintended way, so I suspect this behaviour is a bug.

Expected behavior and actual behavior

Calling groupTuple for process THREE output and ch_three_input should return a valid channel but instead causes a null pointer exception.

Steps to reproduce the problem

Please see the MRE here.

Program output

Error message produced in console:

Cannot invoke method add() on null object

Error message produced in .nextflow.log:

java.lang.NullPointerException: Cannot invoke method add() on null object

See the attached .nextflow.log file for more details.

Environment

• Nextflow version 22.04.0 build 5697
• openjdk 11.0.9.1 2020-11-04 LTS
• macOS Catalina 10.15.7 (19H1824)
• GNU bash, version 5.1.16(1)-release (x86_64-apple-darwin19.6.0)

Also reproduced on Ubuntu, please see above linked GH repository containing MRE.

[robsyme]

This might be a lighter reproducible example:

workflow {
  ch_1 = Channel.of([1, '1a', '1b', '1c'], [2, '2a', '2b', '2c'])
  ch_2 = Channel.of([1, '1c', '1d'], [2, '2e', '2h'])

  ch_1 | mix(ch_2) | groupTuple | view
}

This example also conveniently provides a way to make the bug disappear:

workflow {
  ch_1 = Channel.of([1, '1a', '1b', '1c'], [2, '2a', '2b', '2c'])
  ch_2 = Channel.of([1, '1c', '1d'], [2, '2e', '2h'])

  ch_1 | mix(ch_2) | groupTuple() | view
  ch_1 | mix(ch_2)
}

[stale[bot]]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[pditommaso]

Thanks @robsyme for including a testing example. Fixed by 1d32e2c2.