fix bug when no hto or rna matrix is provided for summary

theislab · Nov 27, 2023 · 2e240ad · 2e240ad
1 parent 66319ab
commit 2e240ad
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Showing 3 changed files with 9 additions and 5 deletions.
diff --git a/bin/donor_match.R b/bin/donor_match.R
@@ -52,6 +52,10 @@ if (!is.null(args$barcode)) {
 
 colname_with_singlet <- colnames(result_csv %>% select_if(~ any(. != "negative" & . != "doublet")))
 colname_with_singlet <- colname_with_singlet[colname_with_singlet != "Barcode"]
+if (length(colname_with_singlet) < 2){
+  stop("Please choose more methods to run donor matching!")
+}
+
 if (!is.null(args$method1) && !is.null(args$method2)) {
   method1_all <- colname_with_singlet[startsWith(colnames(result_csv), args$method1)]
   method2_all <- colname_with_singlet[startsWith(colnames(result_csv), args$method2)]

diff --git a/modules/gene_demultiplexing.nf b/modules/gene_demultiplexing.nf
@@ -62,7 +62,7 @@ process summary{
             if(rna_matrix.name == "None"){
                 error "Error: RNA count matrix is not given."
             }
-            generate_adata = "--generate_anndata --read_rna_mtx $rna_matrix"
+            generate_adata = "--generate_anndata --read_rna_mtx rna_data"
         }
         if (generate_mudata == "True"){
             if(rna_matrix.name == "None"){
@@ -71,10 +71,10 @@ process summary{
             if(hto_matrix.name == "None"){
                 error "Error: HTO count matrix is not given."
             }
-            generate_mdata = "--generate_mudata --read_rna_mtx $rna_matrix --read_hto_mtx $hto_matrix"
+            generate_mdata = "--generate_mudata --read_rna_mtx rna_data --read_hto_mtx hto_data"
         }
         """
-        summary_gene.py $demuxlet_files $vireo_files $souporcell_files $scsplit_files $freemuxlet_files $generate_adata $generate_mdata --sampleId $sampleId
+        summary_gene.py $demuxlet_files $vireo_files $souporcell_files $scsplit_files $freemuxlet_files $generate_adata $generate_mdata
         """
 }
 
@@ -250,7 +250,7 @@ workflow gene_demultiplexing {
 
     Channel.fromPath(params.multi_input) \
                 | splitCsv(header:true) \
-                | map { row-> tuple(row.sampleId, row.hto_matrix_filtered, row.rna_matrix_filtered)}
+                | map { row-> tuple(row.sampleId, file(row.hto_matrix_filtered), file(row.rna_matrix_filtered))}
                 | set {input_list_summary}
     summary(input_list_summary, demuxlet_out, freemuxlet_out, vireo_out, souporcell_out, scSplit_out, 
             params.generate_anndata, params.generate_mudata)

diff --git a/modules/hash_demultiplexing.nf b/modules/hash_demultiplexing.nf
@@ -212,7 +212,7 @@ workflow hash_demultiplexing{
 
     Channel.fromPath(params.multi_input) \
                 | splitCsv(header:true) \
-                | map { row-> tuple(row.sampleId, row.hto_matrix_filtered, row.rna_matrix_filtered)}
+                | map { row-> tuple(row.sampleId, file(row.hto_matrix_filtered), file(row.rna_matrix_filtered))}
                 | set {input_list_summary}
     summary(input_list_summary, demuxem_out, hashsolo_out, htodemux_out, multiseq_out, hashedDrops_out,demuxmix_out,bff_out,gmmDemux_out, params.generate_anndata, params.generate_mudata)