solve p1

pinellolab · Jan 11, 2025 · dab5978 · dab5978
1 parent 5946472
commit dab5978
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Showing 14 changed files with 29 additions and 13 deletions.
diff --git a/bin/prepare_inference.py b/bin/prepare_inference.py
@@ -22,8 +22,7 @@ def main(guide_inference, mudata_path):
 
     # adding 'pairs_to_test' to mudata uns
     ## remove the gene_id that is not included in the mudata
-    mudata.mod['gene'].var['symbol_new'] = mudata.mod['gene'].var['symbol'].str.split('.').str[0]
-    mudata.mod['gene'].var.index = mudata.mod['gene'].var['symbol_new']
+
     gene_var = mudata.mod['gene'].var.index if mudata.mod['gene'].var.index is not None else []
     guide_var = mudata.mod['guide'].var['guide_id'] if mudata.mod['guide'] is not None else []
 

diff --git a/process_mudata_pipeline.nf b/process_mudata_pipeline.nf
@@ -57,19 +57,19 @@ workflow process_mudata_pipeline {
 
     if (params.inference_option == 'predefined_pairs') {
         PrepareInference = prepare_user_guide_inference(
-            file(params.input),
+            Guide_Assignment.guide_assignment_mudata_output,
             file(params.user_inference)
         )}
     else if (params.inference_option == 'by_distance') {
         PrepareInference = prepare_guide_inference(
-            file(params.input),
-            file(params.gtf),
+            Guide_Assignment.guide_assignment_mudata_output,
+            GTF_Reference.gencode_gtf,
             params.distance_from_center
         )}
     else if (params.inference_option == 'all_by_all') {
         PrepareInference = prepare_all_guide_inference(
-            file(params.input),
-            file(params.gtf)
+            Guide_Assignment.guide_assignment_mudata_output,
+            GTF_Reference.gencode_gtf
         )}
 
     if (params.inference_method == "sceptre"){

diff --git a/process_mudata_pipeline_HASHING.nf b/process_mudata_pipeline_HASHING.nf
@@ -80,19 +80,19 @@ workflow process_mudata_pipeline_HASHING {
 
     if (params.inference_option == 'predefined_pairs') {
         PrepareInference = prepare_user_guide_inference(
-            file(params.input),
+            Guide_Assignment.guide_assignment_mudata_output,
             file(params.user_inference)
         )}
     else if (params.inference_option == 'by_distance') {
         PrepareInference = prepare_guide_inference(
-            file(params.input),
-            file(params.gtf),
+            Guide_Assignment.guide_assignment_mudata_output,
+            GTF_Reference.gencode_gtf,
             params.distance_from_center
         )}
     else if (params.inference_option == 'all_by_all') {
         PrepareInference = prepare_all_guide_inference(
-            file(params.input),
-            file(params.gtf)
+            Guide_Assignment.guide_assignment_mudata_output,
+            GTF_Reference.gencode_gtf
         )}
 
     if (params.inference_method == "sceptre"){

diff --git a/processes/downloadGenome.nf b/processes/downloadGenome.nf
@@ -2,7 +2,6 @@
 process downloadGenome {
     input:
     val genome_path
-    val hg38_path
 
     output:
     path "genome.fa.gz" , emit: genome

diff --git a/svg/.DS_Store b/svg/.DS_Store
diff --git a/svg/barplot.svg b/svg/barplot.svg
diff --git a/svg/curve.svg b/svg/curve.svg
diff --git a/svg/knee_plot.svg b/svg/knee_plot.svg
diff --git a/svg/line.svg b/svg/line.svg
diff --git a/svg/network.svg b/svg/network.svg
diff --git a/svg/scatter.svg b/svg/scatter.svg