nf-test test fails currently

[rollf]

Hi,

nf-test test fails for me. Given the error message, it looks like maybe some outdated module is used.

❯ nf-test test

🚀 nf-test 0.9.0
https://www.nf-test.com
(c) 2021 - 2024 Lukas Forer and Sebastian Schoenherr


Test Workflow main.nf

  Test [1394960f] 'Should execute complete pipeline using relative paths' PASSED (77.895s)

Test Process FASTQC

  Test [2628e3dc] 'Should execute fastqc report' PASSED (5.567s)

Test Process SALMON_ALIGN_QUANT

  Test [38c43ad2] 'Should align data using salmon quant' FAILED (5.705s)

  Assertion failed:

  assert process.success
         |       |
         |       false
         SALMON_ALIGN_QUANT

  Nextflow stdout:

  ERROR ~ Error executing process > 'SALMON_ALIGN_QUANT'

  Caused by:
    Process `SALMON_ALIGN_QUANT` terminated with an error exit status (1)

  Command executed:

    salmon quant -i step1_out -l A -1 'reads_1.fq.gz' -2 'reads_2.fq.gz' --validateMappings -o quant

  Command exit status:
    1

  Command output:
    (empty)

  Command error:
    Version Info: ### PLEASE UPGRADE SALMON ###
    ### A newer version of salmon with important bug fixes and improvements is available. ####
    ###
    The newest version, available at https://github.com/COMBINE-lab/salmon/releases
    contains new features, improvements, and bug fixes; please upgrade at your
    earliest convenience.
    ###
    Sign up for the salmon mailing list to hear about new versions, features and updates at:
    https://oceangenomics.com/subscribe
    ###
    ### salmon (mapping-based) v1.0.0
    ### [ program ] => salmon
    ### [ command ] => quant
    ### [ index ] => { step1_out }
    ### [ libType ] => { A }
    ### [ mates1 ] => { reads_1.fq.gz }
    ### [ mates2 ] => { reads_2.fq.gz }
    ### [ validateMappings ] => { }
    ### [ output ] => { quant }
    Logs will be written to quant/logs
    [2024-09-05 10:44:14.664] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
    [2024-09-05 10:44:14.664] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
    [2024-09-05 10:44:14.664] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
    [2024-09-05 10:44:14.664] [jointLog] [info] parsing read library format
    [2024-09-05 10:44:14.664] [jointLog] [info] There is 1 library.
    Exception : [Error: The index version file step1_out/versionInfo.json doesn't seem to exist.  Please try re-building the salmon index.]
    salmon quant was invoked improperly.
    For usage information, try salmon quant --help
    Exiting.

  Work dir:
    /home/rollf/src/nf-test-examples/.nf-test/tests/38c43ad2f48579e65ee894c0874dfcf5/work/54/70a7c4a2e3dc41e09369821faebb7b

  Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

   -- Check '/home/rollf/src/nf-test-examples/.nf-test/tests/38c43ad2f48579e65ee894c0874dfcf5/meta/nextflow.log' file for details
  Nextflow stderr:

  Nextflow 24.04.4 is available - Please consider updating your version to it



Test Process SALMON_INDEX

  Test [27b63f0d] 'Should run without failures' FAILED (4.157s)

  Assertion failed:

  assert process.success
         |       |
         |       false
         SALMON_INDEX

  Nextflow stdout:

  Process `SALMON_INDEX` declares 1 input channel but 0 were specified

   -- Check script '/home/rollf/src/nf-test-examples/.nf-test-27b63f0dd4eb3431ec61c4dc16c0b359.nf' at line: 38 or see '/home/rollf/src/nf-test-examples/.nf-test/tests/27b63f0dd4eb3431ec61c4dc16c0b359/meta/nextflow.log' file for more details
  Nextflow stderr:

  Nextflow 24.04.4 is available - Please consider updating your version to it



Test Workflow RNASEQ

  Test [e4a9ddd6] 'Should run without failures' PASSED (12.086s)


FAILURE: Executed 5 tests in 105.446s (2 failed)