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Merge pull request #17 from frheault/group_approach
Added a group approach
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,256 @@ | ||
| #!/usr/bin/env nextflow | ||
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| if(params.help) { | ||
| usage = file("$baseDir/USAGE") | ||
| cpu_count = Runtime.runtime.availableProcessors() | ||
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| bindings = ["atlas_config":"$params.atlas_config", | ||
| "atlas_directory":"$params.atlas_directory", | ||
| "atlas_centroids":"$params.atlas_centroids", | ||
| "run_average_bundles":"$params.run_average_bundles", | ||
| "multi_parameters":"$params.multi_parameters", | ||
| "minimal_vote_ratio":"$params.minimal_vote_ratio", | ||
| "wb_clustering_thr":"$params.wb_clustering_thr", | ||
| "seeds":"$params.seeds", | ||
| "outlier_alpha":"$params.outlier_alpha", | ||
| "register_processes":"$params.register_processes", | ||
| "rbx_processes":"$params.rbx_processes", | ||
| "cpu_count":"$cpu_count"] | ||
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| engine = new groovy.text.SimpleTemplateEngine() | ||
| template = engine.createTemplate(usage.text).make(bindings) | ||
| print template.toString() | ||
| return | ||
| } | ||
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| log.info "SCIL RecobundlesX pipeline" | ||
| log.info "===========================" | ||
| log.info "" | ||
| log.info "Start time: $workflow.start" | ||
| log.info "" | ||
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| log.debug "[Command-line]" | ||
| log.debug "$workflow.commandLine" | ||
| log.debug "" | ||
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| log.info "[Git Info]" | ||
| log.info "$workflow.repository - $workflow.revision [$workflow.commitId]" | ||
| log.info "" | ||
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| log.info "Options" | ||
| log.info "=======" | ||
| log.info "" | ||
| log.info "[Atlas]" | ||
| log.info "Atlas Config: $params.atlas_config" | ||
| log.info "Atlas Anat: $params.atlas_anat" | ||
| log.info "Atlas Directory: $params.atlas_directory" | ||
| log.info "Atlas Centroids: $params.atlas_centroids" | ||
| log.info "" | ||
| log.info "[Recobundles options]" | ||
| log.info "Multi-Parameters Executions: $params.multi_parameters" | ||
| log.info "Minimal Vote Percentage: $params.minimal_vote_ratio" | ||
| log.info "Whole Brain Clustering Threshold: $params.wb_clustering_thr" | ||
| log.info "Random Seeds: $params.seeds" | ||
| log.info "Outlier Removal Alpha: $params.outlier_alpha" | ||
| log.info "" | ||
| log.info "" | ||
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| log.info "Input: $params.input" | ||
| root = file(params.input) | ||
| /* Watch out, files are ordered alphabetically in channel */ | ||
| tractogram_for_recognition_group = Channel | ||
| .fromFilePairs("$root/**/{*tracking*.*,}", | ||
| size: -1, | ||
| maxDepth:1) {it.parent.name} | ||
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| Channel | ||
| .fromPath("$root/**/*fa.nii.gz", | ||
| maxDepth:1) | ||
| .map{[it.parent.name, it]} | ||
| .into{anat_for_registration;anat_for_reference_centroids;anat_for_reference_bundles_group;anat_for_reference_bundles} | ||
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| Channel | ||
| .fromPath("$params.atlas_directory/*.nii.gz", | ||
| maxDepth:1) | ||
| .into{atlas_anat_for_registration;atlas_anat_for_average} | ||
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| Channel | ||
| .fromPath("$params.atlas_directory/*_group.json", | ||
| maxDepth:1) | ||
| .map{it -> [it.baseName, it]} | ||
| .set{atlas_configs} | ||
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| atlas_config_group = Channel.fromPath("$params.atlas_directory/config_groups.json") | ||
| Channel | ||
| .fromPath("$params.atlas_directory/atlas/", | ||
| maxDepth:1) | ||
| .into{atlas_directory_group;atlas_directory} | ||
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| if (params.atlas_centroids) { | ||
| atlas_centroids = Channel.fromPath("$params.atlas_centroids/*_centroid.trk") | ||
| } | ||
| else { | ||
| atlas_centroids = Channel.empty() | ||
| } | ||
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| workflow.onComplete { | ||
| log.info "Pipeline completed at: $workflow.complete" | ||
| log.info "Execution status: ${ workflow.success ? 'OK' : 'failed' }" | ||
| log.info "Execution duration: $workflow.duration" | ||
| } | ||
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| anat_for_registration | ||
| .combine(atlas_anat_for_registration) | ||
| .set{anats_for_registration} | ||
| process Register_Anat { | ||
| cpus params.register_processes | ||
| memory '2 GB' | ||
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| input: | ||
| set sid, file(native_anat), file(atlas) from anats_for_registration | ||
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| output: | ||
| set sid, "${sid}__output0GenericAffine.mat" into transformation_for_recognition_group, transformation_for_recognition, transformation_for_centroids | ||
| set sid, "${sid}__output0GenericAffine.mat" into transformation_for_average | ||
| file "${sid}__outputWarped.nii.gz" | ||
| file "${sid}__native_anat.nii.gz" | ||
| script: | ||
| """ | ||
| export ANTS_RANDOM_SEED=1234 | ||
| antsRegistrationSyNQuick.sh -d 3 -f ${native_anat} -m ${atlas} -n ${params.register_processes} -o ${sid}__output -t a | ||
| cp ${native_anat} ${sid}__native_anat.nii.gz | ||
| """ | ||
| } | ||
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| anat_for_reference_centroids | ||
| .join(transformation_for_centroids, by: 0) | ||
| .set{anat_and_transformation} | ||
| process Transform_Centroids { | ||
| input: | ||
| set sid, file(anat), file(transfo) from anat_and_transformation | ||
| each file(centroid) from atlas_centroids | ||
| output: | ||
| file "${sid}__${centroid.baseName}.trk" optional true | ||
| script: | ||
| """ | ||
| scil_apply_transform_to_tractogram.py ${centroid} ${anat} ${transfo} tmp.trk --inverse --keep_invalid | ||
| scil_remove_invalid_streamlines.py tmp.trk ${sid}__${centroid.baseName}.trk --cut_invalid --remove_single_point --remove_overlapping_points --no_empty | ||
| """ | ||
| } | ||
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| tractogram_for_recognition_group | ||
| .join(anat_for_reference_bundles_group) | ||
| .join(transformation_for_recognition_group) | ||
| .combine(atlas_config_group) | ||
| .combine(atlas_directory_group) | ||
| .set{tractogram_and_transformation_group} | ||
| process Recognize_Bundles_Group { | ||
| cpus params.rbx_processes | ||
| memory params.rbx_memory_limit | ||
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| input: | ||
| set sid, file(tractograms), file(reference), file(transfo), file(config), file(directory) from tractogram_and_transformation_group | ||
| output: | ||
| set sid, "*.trk" into bundles_for_sub_reco, tmp | ||
| file "results.json" | ||
| file "logfile.txt" | ||
| script: | ||
| """ | ||
| if [ `echo $tractograms | wc -w` -gt 1 ]; then | ||
| scil_streamlines_math.py lazy_concatenate $tractograms tracking_concat.trk | ||
| else | ||
| mv $tractograms tracking_concat.trk | ||
| fi | ||
| scil_remove_invalid_streamlines.py tracking_concat.trk tractogram_ic.trk --reference ${reference} --remove_single_point --remove_overlapping_points | ||
| mkdir tmp/ | ||
| scil_recognize_multi_bundles.py tractogram_ic.trk ${config} ${directory}/*/ ${transfo} --inverse --out_dir tmp/ \ | ||
| --log_level DEBUG --multi_parameters 8 --minimal_vote_ratio 0.5 \ | ||
| --tractogram_clustering_thr 12 15 18 --seeds 0 --processes $params.rbx_processes | ||
| rm tractogram_ic.trk tracking_concat.trk | ||
| mv tmp/* ./ | ||
| """ | ||
| } | ||
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| bundles_for_sub_reco | ||
| .transpose() | ||
| .combine(anat_for_reference_bundles, by: 0) | ||
| .combine(transformation_for_recognition, by: 0) | ||
| .combine(atlas_directory) | ||
| .map{it -> [it[1].baseName, it[0], it[1], it[2], it[3], it[4]]} | ||
| .combine(atlas_configs, by:0) | ||
| .set{tractogram_and_transformation_config} | ||
| process Recognize_Bundles { | ||
| cpus params.rbx_processes | ||
| memory params.rbx_memory_limit | ||
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| input: | ||
| set gName, sid, file(tractogram), file(reference), file(transfo), file(directory), file(config) from tractogram_and_transformation_config | ||
| output: | ||
| set sid, "*.trk" optional true into bundles_for_cleaning | ||
| file "results.json" optional true | ||
| file "logfile.txt" optional true | ||
| script: | ||
| """ | ||
| mkdir tmp/ | ||
| scil_recognize_multi_bundles.py ${tractogram} ${config} ${directory}/*/ ${transfo} --inverse --out_dir tmp/ \ | ||
| --log_level DEBUG --multi_parameters $params.multi_parameters --minimal_vote_ratio $params.minimal_vote_ratio \ | ||
| --tractogram_clustering_thr $params.wb_clustering_thr --seeds $params.seeds --processes $params.rbx_processes | ||
| mv tmp/* ./ | ||
| """ | ||
| } | ||
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| bundles_for_cleaning | ||
| .transpose() | ||
| .set{all_bundles_for_cleaning} | ||
| process Clean_Bundles { | ||
| input: | ||
| set sid, file(bundle) from all_bundles_for_cleaning | ||
| output: | ||
| set sid, val(bname), "${sid}__*_cleaned.trk" optional true into bundle_for_density | ||
| script: | ||
| bname = bundle.name.take(bundle.name.lastIndexOf('.')) | ||
| """ | ||
| scil_outlier_rejection.py ${bundle} "${sid}__${bname}_cleaned.trk" --alpha $params.outlier_alpha | ||
| """ | ||
| } | ||
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| bundle_for_density | ||
| .combine(transformation_for_average, by:0) | ||
| .combine(atlas_anat_for_average) | ||
| .set{all_bundles_transfo_for_average} | ||
| process Compute_Density_Bundles { | ||
| input: | ||
| set sid, val(bname), file(bundle), file(transfo), file(atlas) from all_bundles_transfo_for_average | ||
| output: | ||
| set bname, "*.nii.gz" into bundle_for_average | ||
| when: | ||
| params.run_average_bundles | ||
| script: | ||
| """ | ||
| scil_apply_transform_to_tractogram.py $bundle $atlas $transfo tmp.trk --remove_invalid | ||
| scil_compute_streamlines_density_map.py tmp.trk "${sid}__${bname}_density.nii.gz" | ||
| scil_image_math.py lower_threshold "${sid}__${bname}_density.nii.gz" 1 "${sid}__${bname}_binary.nii.gz" | ||
| """ | ||
| } | ||
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| bundle_for_average | ||
| .flatMap{ sid, bundles -> bundles.collect{[sid, it]} } | ||
| .groupTuple(by: 0) | ||
| .set{all_bundle_for_average} | ||
| process Average_Bundles { | ||
| publishDir = params.Average_Bundles_Publish_Dir | ||
| input: | ||
| set val(bname), file(bundles_bin) from all_bundle_for_average | ||
| output: | ||
| file "${bname}_density.nii.gz" | ||
| file "${bname}_binary.nii.gz" | ||
| script: | ||
| """ | ||
| scil_image_math.py addition *_density.nii.gz 0 ${bname}_density.nii.gz | ||
| scil_image_math.py addition *_binary.nii.gz 0 ${bname}_binary.nii.gz | ||
| """ | ||
| } |
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