Rename deduplication to dedoublet

Mye-InfoBank · Jan 29, 2024 · 7d0484c · 7d0484c
1 parent c10028b
commit 7d0484c
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Showing 3 changed files with 15 additions and 15 deletions.
diff --git a/main.nf b/main.nf
@@ -14,7 +14,7 @@ include { MERGE } from "./modules/merge.nf"
 include { PREPROCESSING } from "./workflows/preprocessing.nf"
 include { COUNTS } from "./workflows/counts.nf"
 include { INTEGRATION } from "./workflows/integration.nf"
-include { DEDUPLICATION } from "./workflows/deduplication.nf"
+include { DOUBLETS } from "./workflows/doublets.nf"
 include { CLUSTERING } from "./workflows/clustering.nf"
 
 if (params.samplesheet) { ch_samplesheet = file(params.samplesheet) } else { exit 1, 'Samplesheet not specified!' }
@@ -44,7 +44,7 @@ workflow {
         Channel.value(params.benchmark_hvgs)
     )
 
-    DEDUPLICATION(
+    DOUBLETS(
         ch_hvgs,
         INTEGRATION.out.scanvi_model,
         INTEGRATION.out.integrated,
@@ -53,22 +53,22 @@ workflow {
     )
 
     CLUSTERING(
-        DEDUPLICATION.out.integrations,
+        DOUBLETS.out.integrations,
         Channel.from(params.leiden_resolutions),
         CELLTYPIST.out,
         Channel.value(params.entropy_initial_smoothness)
     )
 
     ch_obs = CLUSTERING.out.obs.mix(
-        CELL_CYCLE.out, CELLTYPIST.out, DEDUPLICATION.out.solo
+        CELL_CYCLE.out, CELLTYPIST.out, DOUBLETS.out.solo
     )
 
     ch_obsm = CLUSTERING.out.obsm.mix(
-        DEDUPLICATION.out.obsm
+        DOUBLETS.out.obsm
     )
 
     MERGE (
-        DEDUPLICATION.out.raw,
+        DOUBLETS.out.raw,
         COUNTS.out,
         ch_obsm.map{ meta, obsm -> obsm}.collect(),
         ch_obs.map{ meta, obs -> obs}.collect()

diff --git a/modules/deduplicate_adata.nf → modules/dedoublet_adata.nf b/modules/deduplicate_adata.nf → modules/dedoublet_adata.nf
@@ -1,4 +1,4 @@
-process DEDUPLICATE_ADATA {
+process DEDOUBLET_ADATA {
     tag "${meta.id}"
     container "bigdatainbiomedicine/sc-rpy:1.0"
 

diff --git a/workflows/deduplication.nf → workflows/doublets.nf b/workflows/deduplication.nf → workflows/doublets.nf
@@ -1,10 +1,10 @@
 include { SOLO } from "../modules/solo.nf"
-include { DEDUPLICATE_ADATA as DEDUPLICATE_INTEGRATIONS } from "../modules/deduplicate_adata.nf"
-include { DEDUPLICATE_ADATA as DEDUPLICATE_RAW } from "../modules/deduplicate_adata.nf"
+include { DEDOUBLET_ADATA as DEDOUBLET_INTEGRATIONS } from "../modules/dedoublet_adata.nf"
+include { DEDOUBLET_ADATA as DEDOUBLET_RAW } from "../modules/dedoublet_adata.nf"
 include { EXTRACT_EMBEDDING } from "../modules/extract_embedding.nf"
 
 
-workflow DEDUPLICATION {
+workflow DOUBLETS {
     take:
         ch_hvgs
         ch_scanvi_model
@@ -19,21 +19,21 @@ workflow DEDUPLICATION {
             ch_batches
         )
 
-        DEDUPLICATE_INTEGRATIONS(
+        DEDOUBLET_INTEGRATIONS(
             ch_integrations,
             SOLO.out
         )
 
-        EXTRACT_EMBEDDING(DEDUPLICATE_INTEGRATIONS.out)
+        EXTRACT_EMBEDDING(DEDOUBLET_INTEGRATIONS.out)
 
-        DEDUPLICATE_RAW(
+        DEDOUBLET_RAW(
             ch_raw,
             SOLO.out
         )
 
     emit:
         solo = SOLO.out
-        integrations = DEDUPLICATE_INTEGRATIONS.out
-        raw = DEDUPLICATE_RAW.out
+        integrations = DEDOUBLET_INTEGRATIONS.out
+        raw = DEDOUBLET_RAW.out
         obsm = EXTRACT_EMBEDDING.out
 }