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Add error when not enough centroids #11

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merged 3 commits into from
Nov 14, 2022
Merged

Add error when not enough centroids #11

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914d563
Add test to check number of centroids
arnaudbore Sep 1, 2021
259c273
fix merge
Nov 14, 2022
a0735b7
typo
Nov 14, 2022
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20 changes: 16 additions & 4 deletions main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ workflow.onComplete {
Channel
.fromFilePairs("$params.input/**/bundles/*.trk",
size: -1) { it.parent.parent.name }
.set{bundles_for_rm_invalid}
.into{bundles_for_rm_invalid; in_bundles_check}

Channel
.fromFilePairs("$params.input/**/metrics/*.nii.gz",
Expand All @@ -69,6 +69,18 @@ Channel
in_metrics
.set{metrics_for_rename}


in_bundles_check.map{it[1]}.flatten().count().set{number_bundles_for_compare}
in_centroids_check.map{it[1]}.flatten().count().set{number_centroids_for_compare}

if (params.use_provided_centroids){
number_centroids_for_compare
.concat(number_bundles_for_compare)
.toList()
.subscribe{a, b -> if (a < b)
error "Error ~ You ask the pipeline to use provided centroids but there are less centroids than bundles.\nPlease provide at least a centroid per bundle."}
}

process Rename_Metrics {
input:
set sid, file(metrics) from metrics_for_rename
Expand Down Expand Up @@ -208,7 +220,7 @@ process Bundle_Label_And_Distance_Maps {
bname=\$(basename \$bundle .trk)
fi
bname=\${bname/_ic/}

centroid=${sid}__\${bname}_centroid_${params.nb_points}.trk
scil_compute_bundle_voxel_label_map.py \$bundle \${centroid} \
${sid}__\${bname}_labels.nii.gz \
Expand Down Expand Up @@ -305,11 +317,11 @@ process Lesion_Load {
cd streamlines_stats
scil_merge_json.py *.json ../${sid}__lesion_streamlines_stats.json \
--add_parent_key ${sid}

cd ../lesion_load
scil_merge_json.py *.json ../${sid}__lesion_load.json \
--add_parent_key ${sid}

cd ../lesion_load_per_point
scil_merge_json.py *.json ../${sid}__lesion_load_per_point.json \
--add_parent_key ${sid}
Expand Down