making sure all is commited

wtsi-hgi · Oct 23, 2024 · 172a480 · 172a480
1 parent 8080649
commit 172a480
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Showing 3 changed files with 23 additions and 17 deletions.
diff --git a/conf/qc.conf b/conf/qc.conf
@@ -252,6 +252,10 @@ params{
         run_process=false
     }
 
+    seurat_integration{
+        run_process=false
+    }
+
     bbknn{
         run_process = true
         description = 'Parameters for BBKNN'

diff --git a/modules/nf-core/modules/totalVi/main.nf b/modules/nf-core/modules/totalVi/main.nf
@@ -6,7 +6,7 @@ process TOTAL_VI_INTEGRATION{
         label 'process_medium'
     }
 
-    publishDir  path: "${outdir_prev}/clustering/totalVi",
+    publishDir  path: "${outdir_prev}/totalVi",
                 mode: "${params.copy_mode}",
                 overwrite: "true"
 

diff --git a/subworkflows/qc.nf b/subworkflows/qc.nf
@@ -110,24 +110,26 @@ workflow qc {
                 matched_donors.subscribe { println "1:: matched_donors $it" }
                 PREPROCESS_PROCESS(inp4,params.reduced_dims.vars_to_regress.value)
 
-                DSB_INTEGRATE(
-                    PREPROCESS_PROCESS.out.tmp_rsd.collect(),
-                    params.reduced_dims.vars_to_regress.value,
-                    params.reduced_dims.seurat_integration.k_anchor,
-                    params.reduced_dims.seurat_integration.dims,
-                    params.reduced_dims.seurat_integration.ndim_sct,
-                    params.reduced_dims.seurat_integration.ndim_citeBgRemoved,
-                    params.reduced_dims.seurat_integration.ndim_cite_integrated
+                if(params.seurat_integration.run_process){
+                    DSB_INTEGRATE(
+                        PREPROCESS_PROCESS.out.tmp_rsd.collect(),
+                        params.reduced_dims.vars_to_regress.value,
+                        params.reduced_dims.seurat_integration.k_anchor,
+                        params.reduced_dims.seurat_integration.dims,
+                        params.reduced_dims.seurat_integration.ndim_sct,
+                        params.reduced_dims.seurat_integration.ndim_citeBgRemoved,
+                        params.reduced_dims.seurat_integration.ndim_cite_integrated
+                        )
+
+                    MULTIMODAL_INTEGRATION(
+                        DSB_INTEGRATE.out.tmp_rds_file,
                     )
 
-                MULTIMODAL_INTEGRATION(
-                    DSB_INTEGRATE.out.tmp_rds_file,
-                )
-
-                VDJ_INTEGRATION(
-                    chanel_cr_outs.collect(),
-                    MULTIMODAL_INTEGRATION.out.wnn_integrated_file
-                )
+                    VDJ_INTEGRATION(
+                        chanel_cr_outs.collect(),
+                        MULTIMODAL_INTEGRATION.out.wnn_integrated_file
+                    )
+                }
             }