Merge branch 'v1.7'

wtsi-hgi · Oct 23, 2024 · f5832d1 · f5832d1
2 parents bf69c4d + 172a480
commit f5832d1
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Showing 5 changed files with 41 additions and 25 deletions.
diff --git a/bin/totalVI.py b/bin/totalVI.py
@@ -69,7 +69,7 @@
 model = scvi.model.TOTALVI(SLEmap,latent_distribution="normal",n_layers_decoder=2)
 
 model.train()
-model.save("./scvi_model_300samples",adata=SLEmap, overwrite=True)
+model.save("./scvi_model",adata=SLEmap, overwrite=True)
 
 
 # Get latent expression from model: used for UMAP calculations

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
@@ -1,24 +1,30 @@
 process TOTAL_VI_INTEGRATION{
 
     if (params.utilise_gpu){
-        label 'gpu'
+        label 'process_low'
     }else{
         label 'process_medium'
-        label 'process_low'
     }
 
+    publishDir  path: "${outdir_prev}/totalVi",
+                mode: "${params.copy_mode}",
+                overwrite: "true"
+
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "/lustre/scratch123/hgi/teams/hgi/mo11/tmp_projects/sle_project/5.sle_noCB_fullRun_MAD_perPool/yascp_totalvi_v1.sif"
+        container "https://yascp.cog.sanger.ac.uk/public/singularity_images/yascp_totalvi_v1.sif"
     } else {
         container "wtsihgi/nf_scrna_qc:6bb6af5"
     }
 
     input:
         path(adata)
         path(citedata)
+        val(outdir_prev)
 
-    // output:
-    //     val(outdir, emit: outdir)
+    output:
+        path("./figures"), emit: figs, optional: true
+        path("./scvi_model"), emit: scvi_model, optional: true
+        path("./totalVI_integrated.h5ad"), emit: totalVI_integrated, optional: true
 
     script:
 

diff --git a/subworkflows/main_deconvolution.nf b/subworkflows/main_deconvolution.nf
@@ -380,8 +380,12 @@ workflow  main_deconvolution {
         // vir_inp.subscribe { println "vir_inp: $it" }
         vir_inp2 = vir_inp.collect()
         vir_inp3 = vireo_paths.collect()
-        vireo_paths2 = gt_matcher_inp = vir_inp3.combine(vir_inp2)
-
+        vireo_paths2 = gt_matcher_inp = vir_inp3.mix(vir_inp2)
+
+        vireo_paths2.subscribe { println "1:: vireo_paths2 $it" }
+        vir_inp2.subscribe { println "1:: vir_inp2 $it" }
+        vir_inp3.subscribe { println "1:: vir_inp3 $it" }  
+
         GENOTYPE_MATCHER(gt_matcher_inp)
 
         matched_donors = GENOTYPE_MATCHER.out.matched_donors

diff --git a/subworkflows/qc.nf b/subworkflows/qc.nf
@@ -93,7 +93,7 @@ workflow qc {
 
 
                 if(params.totalVi.run_process){
-                    TOTAL_VI_INTEGRATION(NORMALISE_AND_PCA.out.anndata,DSB_PROCESS.out.citeseq_rsd.collect())
+                    TOTAL_VI_INTEGRATION(NORMALISE_AND_PCA.out.anndata,DSB_PROCESS.out.citeseq_rsd.collect(),NORMALISE_AND_PCA.out.outdir)
                 }
 
 
@@ -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
+                    )
+                }
             }