diff --git a/docs/astro/templates/subworkflow.md.jinja2 b/docs/astro/templates/subworkflow.md.jinja2 index 8abe324b..6f27a9d6 100644 --- a/docs/astro/templates/subworkflow.md.jinja2 +++ b/docs/astro/templates/subworkflow.md.jinja2 @@ -40,12 +40,12 @@ head: ### Outputs -| | Type | Description | Optional | Pattern | +| | Type | Description | Mandatory | Pattern | |-|-|-|-|-| {%- for channel in output %} {% for name, content in channel.items() -%} -| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.optional | default(False) }} | {% if content.pattern %} `{{ content.pattern }}` {% endif %} | +| {{ name }} | {{ content.type }} | {{ content.description | channel_descr }} | {{ content.mandatory | default(True) }} | {% if content.pattern %} `{{ content.pattern }}` {% endif %} | {%- endfor %} {%- endfor -%} {% endif %} diff --git a/modules/nf-neuro/reconst/freewater/meta.yml b/modules/nf-neuro/reconst/freewater/meta.yml index 05b88b45..749fcd46 100644 --- a/modules/nf-neuro/reconst/freewater/meta.yml +++ b/modules/nf-neuro/reconst/freewater/meta.yml @@ -56,19 +56,19 @@ input: - para_diff: type: float description: Parallel diffusivity value (diff prior). - optional: true + mandatory: false - iso_diff: type: float description: Isotropic diffusivity value (diff prior). - optional: true + mandatory: false - perp_diff_min: type: float description: Minimum perpendicular diffusivity value (diff prior). - optional: true + mandatory: false - perp_diff_max: type: float description: Maximum perpendicular diffusivity value (diff prior). - optional: true + mandatory: false output: dwi_fw_corrected: - - meta: diff --git a/modules/nf-neuro/reconst/noddi/meta.yml b/modules/nf-neuro/reconst/noddi/meta.yml index b1a6bf79..c30857bd 100644 --- a/modules/nf-neuro/reconst/noddi/meta.yml +++ b/modules/nf-neuro/reconst/noddi/meta.yml @@ -55,11 +55,11 @@ input: - para_diff: type: float description: Parallel diffusivity value (diff prior). - optional: true + mandatory: false - iso_diff: type: float description: Isotropic diffusivity value (diff prior). - optional: true + mandatory: false output: dir: diff --git a/modules/nf-neuro/registration/anattodwi/meta.yml b/modules/nf-neuro/registration/anattodwi/meta.yml index 0f269050..3aaaca04 100644 --- a/modules/nf-neuro/registration/anattodwi/meta.yml +++ b/modules/nf-neuro/registration/anattodwi/meta.yml @@ -185,7 +185,7 @@ output: .gif file containing quality control image for the registration process. For use in MultiQC report. pattern: "*_registration_anattodwi_mqc.gif" - optional: true + mandatory: false ontologies: [] versions: - versions.yml: diff --git a/modules/nf-neuro/registration/ants/meta.yml b/modules/nf-neuro/registration/ants/meta.yml index 26615cae..dbffa2ab 100644 --- a/modules/nf-neuro/registration/ants/meta.yml +++ b/modules/nf-neuro/registration/ants/meta.yml @@ -171,7 +171,7 @@ output: type: file description: Affine transformation from moving to fixed pattern: "*_forward1_affine.mat" - optional: true + mandatory: false ontologies: [] forward_warp: - - meta: @@ -183,7 +183,7 @@ output: type: file description: Nifti volume containing warp field from moving to fixed pattern: "*_forward0_warp.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_3989 # GZIP format backward_warp: @@ -196,7 +196,7 @@ output: type: file description: Nifti volume containing warp field from fixed to moving pattern: "*_backward1_warp.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_3989 # GZIP format backward_affine: @@ -209,7 +209,7 @@ output: type: file description: Affine transformation from fixed to moving pattern: "*_backward0_affine.mat" - optional: true + mandatory: false ontologies: [] forward_image_transform: - - meta: @@ -274,7 +274,7 @@ output: description: .gif file containing quality control image for the registration process. Made for use in MultiQC report. pattern: "*_registration_ants_mqc.gif" - optional: true + mandatory: false ontologies: [] versions: - versions.yml: diff --git a/modules/nf-neuro/registration/antsapplytransforms/meta.yml b/modules/nf-neuro/registration/antsapplytransforms/meta.yml index 1d74146d..d9369bee 100644 --- a/modules/nf-neuro/registration/antsapplytransforms/meta.yml +++ b/modules/nf-neuro/registration/antsapplytransforms/meta.yml @@ -144,7 +144,7 @@ output: .gif file containing quality control image for the registration process. Made for use in MultiQC report. pattern: "*_registration_antsapplytransforms_mqc.gif" - optional: true + mandatory: false ontologies: [] versions: - versions.yml: diff --git a/modules/nf-neuro/registration/easyreg/meta.yml b/modules/nf-neuro/registration/easyreg/meta.yml index 45af4f3a..ffbc2a73 100644 --- a/modules/nf-neuro/registration/easyreg/meta.yml +++ b/modules/nf-neuro/registration/easyreg/meta.yml @@ -93,7 +93,7 @@ output: type: file description: Forward deformation field, composed of all registration stages (affine+deformation). pattern: "*_forward0_warp.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format backward_warp: @@ -106,7 +106,7 @@ output: type: file description: Backward deformation field, composed of all registration stages (inv-deformation+inv-affine). pattern: "*_backward0_warp.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format segmentation_warped: @@ -121,7 +121,7 @@ output: SynthSeg v2 (non-robust) segmentation + parcellation on the warped image. Will produce image only if not passed as input. pattern: "*_warped_segmentation.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format fixed_segmentation_warped: @@ -136,7 +136,7 @@ output: SynthSeg v2 (non-robust) segmentation + parcellation on the reference image. Will produce image only if not passed as input. pattern: "*_warped_reference_segmentation.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format versions: diff --git a/modules/nf-neuro/registration/synthmorph/meta.yml b/modules/nf-neuro/registration/synthmorph/meta.yml index 72c12183..4648aa62 100644 --- a/modules/nf-neuro/registration/synthmorph/meta.yml +++ b/modules/nf-neuro/registration/synthmorph/meta.yml @@ -109,7 +109,7 @@ output: type: file description: Affine transformation matrix to fixed space. pattern: "*_forward{0,1,_standalone}_affine.lta" - optional: true + mandatory: false ontologies: [] forward_warp: - - meta: @@ -121,7 +121,7 @@ output: type: file description: Deformation field to fixed space. pattern: "*_forward0_deform.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format backward_warp: @@ -134,7 +134,7 @@ output: type: file description: Deformation field to moving space. pattern: "*_backward1_deform.nii.gz" - optional: true + mandatory: false ontologies: - edam: http://edamontology.org/format_4001 # NIFTI format backward_affine: @@ -147,7 +147,7 @@ output: type: file description: Affine transformation matrix to moving space. pattern: "*_backward{0,_standalone}_affine.lta" - optional: true + mandatory: false ontologies: [] forward_image_transform: - - meta: diff --git a/subworkflows/nf-neuro/bundle_seg/meta.yml b/subworkflows/nf-neuro/bundle_seg/meta.yml index 28912faf..f7b189bf 100644 --- a/subworkflows/nf-neuro/bundle_seg/meta.yml +++ b/subworkflows/nf-neuro/bundle_seg/meta.yml @@ -82,7 +82,7 @@ output: Channel containing QC data for MultiQC reports. Structure: [ *mqc.* ] pattern: "*mqc.*" - optional: true + mandatory: false - versions: type: file description: | diff --git a/subworkflows/nf-neuro/output_template_space/meta.yml b/subworkflows/nf-neuro/output_template_space/meta.yml index 600370d0..98d6eec5 100644 --- a/subworkflows/nf-neuro/output_template_space/meta.yml +++ b/subworkflows/nf-neuro/output_template_space/meta.yml @@ -125,35 +125,35 @@ output: Channel containing the NIfTI files registered into the template space. Structure: [ val(meta), [path(nifti1), path(nifti2), path(nifti3), ...] ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - ch_registered_mask_files: type: file description: | Channel containing the mask files registered into the template space. Structure: [ val(meta), [path(mask1), path(mask2), path(mask3), ...] ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - ch_registered_labels_files: type: file description: | Channel containing the label files registered into the template space. Structure: [ val(meta), [path(label1), path(label2), path(label3), ...] ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - ch_registered_trk_files: type: file description: | Channel containing the TRK files registered into the template space. Structure: [ val(meta), [path(trk1), path(trk2), path(trk3), ...] ] pattern: "*.trk" - optional: true + mandatory: false - mqc: type: file description: | Channel containing the MultiQC report of the registration. Structure: [ path(mqc) ] pattern: "*mqc.*" - optional: true + mandatory: false - versions: type: file description: | diff --git a/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml b/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml index 7c1759e6..785ad01f 100644 --- a/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml +++ b/subworkflows/nf-neuro/reconst_fw_noddi/meta.yml @@ -83,35 +83,35 @@ output: Nifti file main direction. Structure: [ val(meta), path(dir) ] pattern: "*__fit_dir.nii.gz" - optional: true + mandatory: false - noddi_fwf: type: file description: | Nifti file for Free Water Fraction. Structure: [ val(meta), path(fwf) ] pattern: "*__fit_FWF.nii.gz" - optional: true + mandatory: false - noddi_ndi: type: file description: | Nifti file for Neurite Density Index. Structure: [ val(meta), path(ndi) ] pattern: "*__fit_NDI.nii.gz" - optional: true + mandatory: false - noddi_ecvf: type: file description: | Nifti file for Extra-Cellular Volume Fraction. Structure: [ val(meta), path(ecvf) ] pattern: "*__fit_ECVF.nii.gz" - optional: true + mandatory: false - noddi_odi: type: file description: | Nifti file for Orientation Dispersion Index. Structure: [ val(meta), path(odi) ] pattern: "*__fit_ODI.nii.gz" - optional: true + mandatory: false - versions: type: file description: | diff --git a/subworkflows/nf-neuro/registration/meta.yml b/subworkflows/nf-neuro/registration/meta.yml index 552defb2..1d8fe2be 100644 --- a/subworkflows/nf-neuro/registration/meta.yml +++ b/subworkflows/nf-neuro/registration/meta.yml @@ -105,35 +105,35 @@ output: ONLY PROVIDED BY REGISTRATION_EASYREG. Channel containing the reference image warped in moving space. Structure: [ val(meta), path(image) ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - forward_affine: type: file description: | Channel containing the affine transformation matrix to fixed space. Structure: [ val(meta), path(forward_affine) ] pattern: "*__forward*.{lta,mat}" - optional: true + mandatory: false - forward_warp: type: file description: | Channel containing the deformation field to fixed space. Structure: [ val(meta), path(forward_warp) ] pattern: "*__forward*.{nii,nii.gz}" - optional: true + mandatory: false - backward_warp: type: file description: | Channel containing the deformation field to moving space. Structure: [ val(meta), path(backward_warp) ] pattern: "*__backward*.{nii,nii.gz}" - optional: true + mandatory: false - backward_affine: type: file description: | Channel containing the affine transformation matrix to moving space. Structure: [ val(meta), path(backward_affine) ] pattern: "*__backward*.{lta,mat}" - optional: true + mandatory: false - forward_image_transform: type: list description: | @@ -169,7 +169,7 @@ output: segmentation + parcellation in moving space (floating in Easyreg naming convention). Structure: [ val(meta), path(segmentation) ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - reference_segmentation: type: file description: | @@ -177,14 +177,14 @@ output: segmentation + parcellation in fixed space (reference in Easyreg naming convention). Structure: [ val(meta), path(reference_segmentation) ] pattern: "*.{nii,nii.gz}" - optional: true + mandatory: false - mqc: type: file description: | Channel containing the MultiQC report data for the registration. Structure: [ path(mqc) ] pattern: "*mqc.*" - optional: true + mandatory: false - versions: type: file description: |