scilus / dmriqc_flow Goto Github PK

I tried running this today. I updated nextlfow (nextflow self-update) and ran this locally and got:

WARN: Nextflow version 22.04.5 does not match workflow required version: 21.1+ -- Execution will continue, but things may break!
This workflow requires Nextflow version 21.0 or greater -- You are running version 22.04.5

I saw after that you suggest using 21.1. But currently, message says 21.0 or greater, so I simply updated without checking the github or readme. Message should be "but not higher than"., or add a check;

if( !nextflow.version.matches('22.0+') ) {
    error "This workflow requires Nextflow version 21.*. -- You are running nextflow.version. Suggestion: Use 
            >>> NXF_VER=21.10.6 nextflow run dmriqc_flow/main.nf  [...] "
}

I just ran dmriqc_flow (the current master version) on tractoflow output and it skipped the Eddy_topup folder for some reason.

I my case, I ran tractoflow with: run_denoise_dwi false, topup false, eddy false. I still had the Bet on the DWI.

During QC, however, the QC_Brain_Extraction_DWI does not run. I checked why. It uses dwi_mask_for_bet, which comes from dwi_eddy_for_bet, which is created with:

Channel
   .fromPath(["$input/**/Eddy/*dwi_corrected.nii.gz", "$input/**/Eddy_Topup/*dwi_corrected.nii.gz"], maxDepth:3)
   .collect(sort:true)
   .map{[it]}
   .set{dwi_eddy_for_bet}

But I have none of these files.