Merge pull request #51 from rikenbit/dev

Dev

CHANGELOG.md

@@ -5,6 +5,12 @@
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v1.4.1 (`-r 1.4.1`) [2021-09-09]
+
+### `v1.4.1 Fixed`
+
+- Fixed the problem that dimensional reduction plots are not displayed in the MulitiQC report
+
 ## v1.4 (`-r 1.4`) [2021-08-23]
 
 ### `v1.4 Added`

bin/drawplot_tpm_counts.r

@@ -113,34 +113,34 @@ if (tool_name=="fcounts"){
     countdata_pca_data = create_pca_tsne_umap_mode(countdata_log, mode="pca", perplexity=10, local_connectivity=1.0, n_neighbors=15)
 
     if (!is.null(countdata_pca_data)){
-      g1 = ggplot_2D(countdata_pca_data[["data_df"]], "PC1", "PC2", "pcaplot_tpm_allsample", "")
-      ggsave(file = "pcaplot_tpm_allsample.pdf", plot=g1, dpi=100, width=8, height=7)
+      g1 = ggplot_2D(countdata_pca_data[["data_df"]], "PC1", "PC2", "DRplot_pca_allsample", "")
+      ggsave(file = "DRplot_pca_allsample.pdf", plot=g1, dpi=100, width=8, height=7)
       outputdata = countdata_pca_data[["data_df"]][,1:2]
       rownames(outputdata) = colnames(countdata_log)
-      write.csv(outputdata, 'pcaplot_tpm_allsample.csv', quote=FALSE, append=TRUE)
+      write.csv(outputdata, 'DRplot_pca_allsample.csv', quote=FALSE, append=TRUE)
     } 
 
     ### draw tsneplot
     countdata_tsne_data = create_pca_tsne_umap_mode(countdata_log, mode="tsne", perplexity=10, local_connectivity=1.0, n_neighbors=15)  
 
     if (!is.null(countdata_tsne_data)){
-      g2 = ggplot_2D(countdata_tsne_data[["data_df"]], "V1", "V2", "tsneplot_tpm_allsample", "")
-      ggsave(file = "tsneplot_tpm_allsample.pdf", plot=g2, dpi=100, width=8, height=7)  
+      g2 = ggplot_2D(countdata_tsne_data[["data_df"]], "V1", "V2", "DRplot_tsne_allsample", "")
+      ggsave(file = "DRplot_tsne_allsample.pdf", plot=g2, dpi=100, width=8, height=7)  
 
       outputdata = countdata_tsne_data[["data_df"]][,1:2]
       rownames(outputdata) = colnames(countdata_log)
-      write.csv(outputdata, 'tsneplot_tpm_allsample.csv', quote=FALSE, append=TRUE)
+      write.csv(outputdata, 'DRplot_tsne_allsample.csv', quote=FALSE, append=TRUE)
     } 
 
     ### draw umapplot
     countdata_umap_data = create_pca_tsne_umap_mode(countdata_log, mode="umap", perplexity=10, local_connectivity=1.0, n_neighbors=15)  
 
     if (!is.null(countdata_umap_data)){
-      g3 = ggplot_2D(countdata_umap_data[["data_df"]], "V1", "V2", "umapplot_tpm_allsample", "")
-      ggsave(file = "umapplot_tpm_allsample.pdf", plot=g3, dpi=100, width=8, height=7)
+      g3 = ggplot_2D(countdata_umap_data[["data_df"]], "V1", "V2", "DRplot_umap_allsample", "")
+      ggsave(file = "DRplot_umap_allsample.pdf", plot=g3, dpi=100, width=8, height=7)
       outputdata = countdata_umap_data[["data_df"]][,1:2]
       rownames(outputdata) = colnames(countdata_log)
-      write.csv(outputdata, 'umapplot_tpm_allsample.csv', quote=FALSE, append=TRUE)
+      write.csv(outputdata, 'DRplot_umap_allsample.csv', quote=FALSE, append=TRUE)
     } 
   }
 }

main.nf

@@ -1918,6 +1918,7 @@ process create_plots_fromTPM {
 
     output:
     file "*.{txt,pdf}" into plots_from_tpmcounts_results
+    file "DRplot_*.csv" into tpmcounts_DRplot
     file "barplot_*.csv" into tpmcounts_barplot
     file "gstat_*.csv" into tpmcounts_gstat
 
@@ -1930,19 +1931,19 @@ process create_plots_fromTPM {
     cat $detgene_header_gstat gstat_num_of_detectedgene.csv >> tmp_file
     mv tmp_file gstat_num_of_detectedgene_mqc.csv
     
-    if [[ -f pcaplot_tpm_allsample.csv ]]; then
-        cat $pcaplot_header pcaplot_tpm_allsample.csv >> tmp_file
-        mv tmp_file pcaplot_tpm_allsample_mqc.csv
+    if [[ -f DRplot_pca_allsample.csv ]]; then
+        cat $pcaplot_header DRplot_pca_allsample.csv >> tmp_file
+        mv tmp_file DRplot_pca_allsample_mqc.csv
     fi
     
-    if [[ -f tsneplot_tpm_allsample.csv ]]; then
-        cat $tsneplot_header tsneplot_tpm_allsample.csv >> tmp_file
-        mv tmp_file tsneplot_tpm_allsample_mqc.csv
+    if [[ -f DRplot_tsne_allsample.csv ]]; then
+        cat $tsneplot_header DRplot_tsne_allsample.csv >> tmp_file
+        mv tmp_file DRplot_tsne_allsample_mqc.csv
     fi
 
-    if [[ -f umapplot_tpm_allsample.csv ]]; then
-        cat $umapplot_header umapplot_tpm_allsample.csv >> tmp_file
-        mv tmp_file umapplot_tpm_allsample_mqc.csv
+    if [[ -f DRplot_umap_allsample.csv ]]; then
+        cat $umapplot_header DRplot_umap_allsample.csv >> tmp_file
+        mv tmp_file DRplot_umap_allsample_mqc.csv
     fi
     
     """
@@ -2071,6 +2072,7 @@ process multiqc {
     file ('plots_bar_fcounts_histone/*') from fcounts_histone_barplot.collect().ifEmpty([]) 
     file ('plots_bar_fcounts_histone/*') from fcounts_histone_gstat.collect().ifEmpty([]) 
     file ('plots_from_tpmcounts/*') from plots_from_tpmcounts_results.collect().ifEmpty([])
+    file ('plots_from_tpmcounts/*') from tpmcounts_DRplot.collect().ifEmpty([])
     file ('plots_from_tpmcounts/*') from tpmcounts_barplot.collect().ifEmpty([])
     file ('plots_from_tpmcounts/*') from tpmcounts_gstat.collect().ifEmpty([])
     file ('plots_from_tpmcounts_rsem/*') from rsem_gene_barplot.collect().ifEmpty([])

nextflow.config

@@ -163,7 +163,7 @@ manifest {
   description = 'This pipeline analyses data from full-length single-cell RNA sequencing (scRNA-seq) methods.'
   mainScript = 'main.nf'
   nextflowVersion = '>=19.10.0'
-  version = '1.4'
+  version = '1.4.1'
 }
 
 // Function to ensure that resource requirements don't go beyond