Nextflow pipeline stopping after MP2RAGE processing

[mathieuboudreau]

It seems to tell me the run is successful, but only the first (MP2RAGE) step appears to have run on the subjects.

(base) mathieuboudreau@Mathieus-MacBook-Pro anat-processing % nextflow -log $TMPDIR/cneuromod.log run neuromod-process-anat.nf --bids anat/ -w $TMPDIR -with-report ./report.html 
N E X T F L O W  ~  version 22.04.4
Launching `neuromod-process-anat.nf` [extravagant_caravaggio] DSL2 - revision: e5bdc6d0f7
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Using Octave in Docker or (if local) from the sys path.
Session-level organization has been ENABLED.
Input: anat/
Derivatives: anat//derivatives/qMRLab
Nextflow Work Dir: /var/folders/l1/1xswjffd73l8yp7dd7pq9lyw0000gn/T
executor >  local (62)
[a5/bb15a2] process > fitMp2rageUni (sub-03_ses-005) [100%] 62 of 62 ✔
[-        ] process > alignMtsatInputs               -
[-        ] process > extractBrain                   -
[-        ] process > resampleB1                     -
[-        ] process > smoothB1WithMask               -
[-        ] process > smoothB1WithoutMask            -
[-        ] process > fitMtsatWithB1Mask             -
[-        ] process > fitMtsatWithB1                 -
[-        ] process > fitMtsatWithBet                -
[-        ] process > fitMtsat                       -
[-        ] process > fitMtratio                     -
[-        ] process > generateRegionMasks            -
[-        ] process > publishOutputs                 -
[-        ] process > publishOutputsFmap             -
[-        ] process > publishOutputsMasks            -
Pipeline completed at: 2022-06-22T14:07:21.953678-03:00
Execution status: OK
Execution duration: 35m 32s
Mnemonic ID: extravagant_caravaggio
Completed at: 22-Jun-2022 14:07:24
Duration    : 35m 35s
CPU hours   : 2.8
Succeeded   : 62

(base) mathieuboudreau@Mathieus-MacBook-Pro anat-processing %

[mathieuboudreau]

I don't have access to the assignees list, so tagging @agahkarakuzu.

[mathieuboudreau]

The results file also shows that only MP2RAGE was processed.