Expimap Intr_cvae now use condition_col instead of batch_col, dependencies changed a bit

Author: gregothebyteknight

modules/local/scarches/expimap/environment.yml

@@ -2,8 +2,6 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - python=3.14
   - pip
   - pip:
-    - scArches==0.6.1
-    - anndata==0.9.2
+    - scArches=0.6.1

modules/local/scarches/expimap/main.nf

@@ -10,7 +10,7 @@ process SCARCHES_EXPIMAP {
     input:
     tuple val(meta), path(h5ad, arity: 1)
     tuple val(meta2), path(reference_model)
-    val(batch_col)
+    val(condition_col)
     val(counts_layer)
 
     output:

modules/local/scarches/expimap/templates/expimap.py

@@ -32,7 +32,7 @@
 # Initialization of the model with the reference network
 intr_cvae = sca.models.EXPIMAP(
     adata=adata_processing,
-    condition_key="${batch_col}",
+    condition_key="${condition_col}",
     hidden_layer_sizes=[256, 256, 256],
     recon_loss="nb"
 )

modules/local/scarches/expimap/tests/main.nf.test

@@ -25,7 +25,7 @@ nextflow_process {
                         file("${projectDir}/assets/databases/expimap/pathways.gmt", checkIfExists: true)
                     ]
                 )
-                input[2] = 'sample'
+                input[2] = 'condition'
                 input[3] = 'X'
                 """
             }
@@ -62,7 +62,7 @@ nextflow_process {
                     ]
                 )
                 input[1] = [[], []]
-                input[2] = 'sample'
+                input[2] = 'condition'
                 input[3] = 'X'
                 """
             }

subworkflows/local/combine/main.nf

@@ -17,6 +17,7 @@ workflow COMBINE {
     scvi_continuous_covariates  //   value: string
     scimilarity_model           //   value: string
     expimap_gmt                 //   value: string
+    condition_col               //   value: string
 
     main:
 
@@ -49,7 +50,8 @@ workflow COMBINE {
         scvi_categorical_covariates,
         scvi_continuous_covariates,
         scimilarity_model,
-        expimap_gmt
+        expimap_gmt,
+        condition_col
     )
     ch_versions      = ch_versions.mix(INTEGRATE.out.versions)
     ch_var           = ch_var.mix(INTEGRATE.out.var)

subworkflows/local/integrate/main.nf

@@ -25,6 +25,7 @@ workflow INTEGRATE {
     scvi_continuous_covariates  // list of string
     scimilarity_model           // path
     expimap_gmt                 // path
+    condition_col               // string
 
     main:
     ch_versions = channel.empty()
@@ -155,7 +156,7 @@ workflow INTEGRATE {
             expimap_gmt
             ? channel.value([[id: 'expimap'], file(expimap_gmt, checkIfExists: true)])
             : channel.value([[id: 'expimap'], file("${projectDir}/assets/databases/expimap/pathways.gmt", checkIfExists: true)]),
-            "batch",
+            condition_col,
             "X"
         )
         ch_versions = ch_versions.mix(SCARCHES_EXPIMAP.out.versions)

workflows/scdownstream.nf

@@ -155,6 +155,9 @@ workflow SCDOWNSTREAM {
             //
             // Combine samples and perform integration
             //
+            grouping_col = "label"
+            condition_col = "condition"
+
             COMBINE (
                 ch_h5ad,
                 ch_base,
@@ -168,6 +171,7 @@ workflow SCDOWNSTREAM {
                 scvi_continuous_covariates,
                 scimilarity_model,
                 expimap_gmt,
+                condition_col,
             )
             ch_versions = ch_versions.mix(COMBINE.out.versions)
             ch_obs = ch_obs.mix(COMBINE.out.obs)
@@ -177,8 +181,6 @@ workflow SCDOWNSTREAM {
             ch_finalization_base = COMBINE.out.h5ad
 
             ch_label_grouping = COMBINE.out.h5ad_inner
-            grouping_col = "label"
-            condition_col = "condition"
         }
     }
     else {