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add profile only_preprocessing #95

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8 changes: 4 additions & 4 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -1724,7 +1724,7 @@ process PFT_Tracking_Maps {
set sid, "${sid}__interface.nii.gz" into interface_for_pft_seeding_mask

when:
params.run_pft_tracking
params.run_pft_tracking || params.run_pft_mask

script:
"""
Expand Down Expand Up @@ -1752,7 +1752,7 @@ process PFT_Seeding_Mask {
set sid, "${sid}__pft_seeding_mask.nii.gz" into seeding_mask_for_pft

when:
params.run_pft_tracking
params.run_pft_tracking || params.run_pft_mask

script:
if (params.pft_seeding_mask_type == "wm")
Expand Down Expand Up @@ -1831,7 +1831,7 @@ process Local_Tracking_Mask {
set sid, "${sid}__local_tracking_mask.nii.gz" into tracking_mask_for_local

when:
params.run_local_tracking
params.run_local_tracking || params.run_local_mask

script:
if (params.local_tracking_mask_type == "wm")
Expand Down Expand Up @@ -1862,7 +1862,7 @@ process Local_Seeding_Mask {
set sid, "${sid}__local_seeding_mask.nii.gz" into tracking_seeding_mask_for_local

when:
params.run_local_tracking
params.run_local_tracking || params.run_local_mask

script:
if (params.local_seeding_mask_type == "wm")
Expand Down
9 changes: 9 additions & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -96,6 +96,7 @@ params {
min_md_in_ventricle=0.003

//**PFT seeding mask**//
run_pft_mask=false
pft_seeding_mask_type="wm"
pft_fa_seeding_mask_threshold=0.1

Expand All @@ -118,6 +119,7 @@ params {
pft_random_seed=0

//**Local seeding mask**//
run_local_mask=false
local_seeding_mask_type="wm"
local_fa_seeding_mask_threshold=0.1

Expand Down Expand Up @@ -223,6 +225,13 @@ profiles {
}
}

only_preprocessing {
params.run_local_tracking=false
params.run_pft_tracking=false
params.run_local_mask=true
params.run_pft_mask=true
}

macos {
process.scratch="/tmp"
}
Expand Down