Merge pull request #32 from theislab/docs

Fix bug when no hto or rna matrix is provided for summary
theislab · Nov 27, 2023 · 94067fd · 94067fd
2 parents 1d4f0bc + e3c949c
commit 94067fd
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Showing 4 changed files with 10 additions and 7 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_demulti/freemuxlet.nf b/modules/gene_demulti/freemuxlet.nf
@@ -74,8 +74,7 @@ process freemuxlet {
         mkdir freemuxlet_${sampleId}
         mkdir freemuxlet_${sampleId}/plp
         touch freemuxlet_${sampleId}/params.csv
-        barcode_num=\$(wc -l < "${group_list}")
-        echo -e "Argument,Value \n samfile,${sam} \n tag_group,${tag_group} \n tag_UMI,${tag_UMI} \n vcf_file,${vcf} \n sm,${sm} \n sm_list_file,${sm_list_file_name} \n sam_verbose,${sam_verbose} \n vcf_verbose,${vcf_verbose} \n skip_umi,${skip_umi} \n cap_BQ,${cap_BQ} \n min_BQ,${min_BQ} \n min_MQ,${min_MQ} \n min_TD,${min_TD} \n excl_flag,${excl_flag} \n grouplist,${grouplist.name}_\${barcode_num} \n min_total,${min_total} \n min_uniq,${min_uniq} \n min_umi,${min_umi} \n min_snp,${min_snp} \n init_cluster,${init_cluster} \n nsample,${nsample} \n aux_files,${aux_files} \n verbose,${verbose} \n doublet_prior,${doublet_prior} \n bf_thres,${bf_thres} \n frac_init_clust,${frac_init_clust} \n iter_init,${iter_init} \n keep_init_missing,${keep_init_missing}" >> freemuxlet_${sampleId}/params.csv
+        echo -e "Argument,Value \n samfile,${sam} \n tag_group,${tag_group} \n tag_UMI,${tag_UMI} \n vcf_file,${vcf} \n sm,${sm} \n sm_list_file,${sm_list_file_name} \n sam_verbose,${sam_verbose} \n vcf_verbose,${vcf_verbose} \n skip_umi,${skip_umi} \n cap_BQ,${cap_BQ} \n min_BQ,${min_BQ} \n min_MQ,${min_MQ} \n min_TD,${min_TD} \n excl_flag,${excl_flag} \n grouplist,${group_list} \n min_total,${min_total} \n min_uniq,${min_uniq} \n min_umi,${min_umi} \n min_snp,${min_snp} \n init_cluster,${init_cluster} \n nsample,${nsample} \n aux_files,${aux_files} \n verbose,${verbose} \n doublet_prior,${doublet_prior} \n bf_thres,${bf_thres} \n frac_init_clust,${frac_init_clust} \n iter_init,${iter_init} \n keep_init_missing,${keep_init_missing}" >> freemuxlet_${sampleId}/params.csv
         
         popscle dsc-pileup $samfile ${taggroup} ${tagUMI} $vcffile ${smlist} ${sm_list_file} ${samverbose} ${vcfverbose} \
             ${skipumi} ${capBQ} ${minBQ} ${minMQ} ${minTD} ${exclflag} ${grouplist} ${mintotal} ${minuniq} ${minsnp} \

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)