pft tracking fix to restore cache

Author: AlexVCaron

modules/nf-neuro/preproc/n4/main.nf

@@ -23,7 +23,7 @@ process PREPROC_N4 {
     def bspline_knot_per_voxel = task.ext.bspline_knot_per_voxel ? "$task.ext.bspline_knot_per_voxel" : "1"
     def shrink_factor = task.ext.shrink_factor ? "$task.ext.shrink_factor" : "1"
     """
-    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
     export ANTS_RANDOM_SEED=1234

modules/nf-neuro/tracking/pfttracking/main.nf

@@ -54,9 +54,9 @@ process TRACKING_PFTTRACKING {
         --interface ${prefix}__interface.nii.gz -f
 
     if [ "${pft_seeding_mask}" == "wm" ]; then
-        scil_volume_math.py convert $wm ${prefix}__mask_wm.nii.gz \
+        scil_volume_math.py convert $wm ${prefix}__pft_seeding_mask.nii.gz \
             --data_type uint8 -f
-        scil_volume_math.py union ${prefix}__mask_wm.nii.gz \
+        scil_volume_math.py union ${prefix}__pft_seeding_mask.nii.gz \
             ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz\
             --data_type uint8 -f
 

subworkflows/local/utils_nfcore_nf-tractoflow_pipeline/main.nf

@@ -117,10 +117,8 @@ workflow PIPELINE_INITIALISATION {
         ch_samplesheet = ch_samplesheet.mix(ch_bids_sheets)
     }
 
-    IO_SAFECASTINPUTS( ch_samplesheet )
-
     emit:
-    samplesheet = IO_SAFECASTINPUTS.out.safe_inputs
+    samplesheet = ch_samplesheet
     versions    = ch_versions
 }
 

workflows/nf-tractoflow.nf

@@ -7,11 +7,7 @@ include { MULTIQC                } from '../modules/nf-core/multiqc/main'
 include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'
-include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_tractoflow_pipeline'
-include { TRACTOFLOW as RUN } from '../subworkflows/nf-neuro/tractoflow'
-include { RECONST_SHSIGNAL } from '../modules/local/reconst/shsignal'
-
-
+include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nf-tractoflow_pipeline'
 include { TRACTOFLOW as RUN } from '../subworkflows/nf-neuro/tractoflow'
 include { RECONST_SHSIGNAL } from '../modules/local/reconst/shsignal'