Invalid `tuple` output parameter declaration

[gentlezr]

The base information as flow:
$nextflow info
Version: 19.10.0 build 5170
Created: 21-10-2019 15:07 UTC (23:07 CDT)
System: Linux 6.11.0-29-generic
Runtime: Groovy 2.5.8 on OpenJDK 64-Bit Server VM 11.0.27+6
Encoding: UTF-8 (UTF-8)

$ apptainer --version
apptainer version 1.4.2

$tree input
input/
└── s1
├── bval
├── bvec
├── dwi.nii.gz
└── t1.nii.gz

The cmd line I used is: run tractoflow -r 2.4.3 --input ./input -with-singularity ~/Downloads/scilus_2.1.0.sif

After I ran the line and got this err msg:

TractoFlow pipeline

Start time: 2025-09-04T13:27:53.603889+08:00

Max DTI shell extracted: 1200
Min FODF shell extracted: 700
Input: ./input
executor > local (1)
[- ] process > README -
[97/88261c] process > Bet_Prelim_DWI (s1) [ 0%] 0 of 1
[- ] process > Denoise_DWI -
[- ] process > Gibbs_correction -
[- ] process > Prepare_for_Topup -
[- ] process > Topup -
Invalid tuple output parameter declaration -- item: nextflow.script.TokenEnvCall(nextflow.script.TokenVar(rev_number_dir))

Could you please help me to solve this problem?

[gentlezr]

The related log file is:

9月-04 13:27:54.280 [Task submitter] INFO nextflow.Session - [97/88261c] Submitted process > Bet_Prelim_DWI (s1)
9月-04 13:27:54.281 [main] DEBUG nextflow.Session - Session aborted -- Cause: Invalid tuple output parameter declaration -- item: nextflow.script.TokenEnvCall(nextflow.script.TokenVar(rev_number_dir))
9月-04 13:27:54.296 [main] DEBUG nextflow.Session - The following nodes are still active:
[process] Gibbs_correction
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $

[process] Prepare_for_Topup
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $

[process] Topup
status=ACTIVE
port 0: (queue) OPEN ; channel: -
port 1: (cntrl) - ; channel: $

9月-04 13:27:54.299 [main] ERROR nextflow.cli.Launcher - Invalid tuple output parameter declaration -- item: nextflow.script.TokenEnvCall(nextflow.script.TokenVar(rev_number_dir))
java.lang.IllegalArgumentException: Invalid tuple output parameter declaration -- item: nextflow.script.TokenEnvCall(nextflow.script.TokenVar(rev_number_dir))

[gentlezr]

I change the nextflow version to 21.10.0 build 5640 the pipline can run but some steps made mistakes and are ignored.

[gentlezr]

New err found, I think it can be solved by degrading the apptainer image sif version I will try.

usage: scil_extract_b0.py [-h]
[--all | --mean | --cluster-mean | --cluster-first]
[--block-size INT] [--single-image]
[--b0_threshold thr] [--skip_b0_check]
[-v [{DEBUG,INFO,WARNING}]] [-f]
in_dwi in_bval in_bvec out_b0
scil_extract_b0.py: error: unrecognized arguments: --force_b0_threshold

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Yeah 1.6.0 is OKAY!