Seperate DE files required for the report and to be output to the user

bin/workflow_glue/de_plots.py

@@ -237,29 +237,29 @@ def dtu_section(dtu_file, section, gt_dic, ge_dic):
     section.table(dtu_results.loc[dtu_pvals.index])
 
 
-def add_gene_names_dge(dge_file, geid_gname):
+def copy_dge_add_gene_names(dge_file, geid_gname, newfile_name):
     """Add gene name column to DGE TSV with gene ID to gene Name dict."""
     dge_results = pd.read_csv(dge_file, sep='\t')
     column_to_move = dge_results.index.map(
         lambda x: geid_gname.get(x))
     dge_results.insert(0, "gene_name", column_to_move)
-    dge_results.to_csv(dge_file, index=True, index_label="gene_id",  sep="\t")
+    dge_results.to_csv(newfile_name, index=True, index_label="gene_id",  sep="\t")
 
 
-def add_gene_names_filtered(unfiltered_file, geid_gname):
+def copy_filtered_add_gene_names(unfiltered_file, geid_gname, newfile_name):
     """Use gene id to gene name dict to add name column to counts TSV."""
     unfiltered = pd.read_csv(unfiltered_file, sep='\t')
     unfiltered.insert(1, "gene_name",  unfiltered.gene_id.map(
         lambda x: geid_gname.get(x)))
-    unfiltered.to_csv(unfiltered_file, index=False, sep='\t')
+    unfiltered.to_csv(newfile_name, index=False, sep='\t')
 
 
-def add_tpm_names(tpm_file, txid_gname):
-    """Use transcript id to gene name dict to add gname column to TPM TSV."""
+def copy_tpm_add_gene_names(tpm_file, txid_gname, newfile_name):
+    """Use transcript id to gene name dict to add name column to TPM TSV."""
     tpm = pd.read_csv(tpm_file, sep='\t')
     tpm.insert(1, "gene_name", tpm.Reference.map(
         lambda x: txid_gname.get(x)))
-    tpm.to_csv(tpm_file, index=False, sep='\t')
+    tpm.to_csv(newfile_name, index=False, sep='\t')
 
 
 def dge_section(dge_file, section, ids_dic):
@@ -404,13 +404,14 @@ Find the full sequences of any transcripts in the
     section.table(alignment_summary_df, key='alignment-stats', index=True)
     salmon_table(tpm, section)
     gene_txid, gene_name, geid_gname = get_translations(stringtie)
-
     # Use dictionaries to add gene names to the counts tsv files to help users
-    add_gene_names_dge(dge, geid_gname)
-    add_gene_names_dge(gene_counts, geid_gname)
-    add_gene_names_filtered(filtered, geid_gname)
-    add_gene_names_filtered(unfiltered, geid_gname)
-    add_tpm_names(tpm, gene_txid)
+    copy_dge_add_gene_names(dge, geid_gname, "results_dge.tsv")
+    copy_dge_add_gene_names(gene_counts, geid_gname, "all_gene_counts.tsv")
+    copy_filtered_add_gene_names(
+        filtered, geid_gname, "filtered_transcript_counts_with_genes.tsv")
+    copy_filtered_add_gene_names(
+        unfiltered, geid_gname, "unfiltered_transcript_counts_with_genes.tsv")
+    copy_tpm_add_gene_names(tpm, gene_txid, "unfiltered_tpm_transcript_counts.tsv")
 
     # Add tables to report
     dge_section(dge, section, gene_name)

main.nf

@@ -407,10 +407,13 @@ process makeReport {
         path "seqkit/*"
         path "isoforms_table/*"
     output:
-        path("wf-transcriptomes-*.html"), emit: report
-        // for DE analysis, a `gene_name` column will be added to
-        // `de_report/results_dge.tsv`
-        path "results_dge.tsv", emit: de_analysis, optional: true
+        path ("wf-transcriptomes-*.html"), emit: report
+        // If de analysis has been run output the counts files with gene name added.
+        path ("results_dge.tsv"), emit: results_dge, optional: true
+        path ("unfiltered_tpm_transcript_counts.tsv"), emit: tpm, optional: true
+        path ("unfiltered_transcript_counts_with_genes.tsv"), emit: unfiltered, optional: true
+        path ("filtered_transcript_counts_with_genes.tsv"), emit: filtered, optional: true
+        path ("all_gene_counts.tsv"), emit: gene_counts, optional: true
     shell:
         // Convert the sample_id arrayList.
         sids = new BlankSeparatedList(sample_ids)
@@ -691,7 +694,7 @@ workflow pipeline {
 
        report = makeReport.out.report
 
-       results = results.concat(makeReport.out.report)
+       results = results.concat(report)
        
        if (use_ref_ann){
             results = run_gffcompare.output.gffcmp_dir.concat(
@@ -719,8 +722,12 @@ workflow pipeline {
        results = results.map{ [it, null] }.concat(fastq_ingress_results.map { [it, "fastq_ingress_results"] })
         
         if (params.de_analysis){
-           de_update = makeReport.out.de_analysis
-           de_results = report.concat(transcriptome, de_outputs.flatten(), counts.flatten(), de_update)
+           de_results = report.concat(
+            transcriptome, de_outputs.flatten(), counts.flatten(),
+            makeReport.out.results_dge,  makeReport.out.tpm, 
+            makeReport.out.filtered,  makeReport.out.unfiltered, 
+            makeReport.out.gene_counts)
+            // Output de_analysis results in the dedicated directory.
             results = results.concat(de_results.map{ [it, "de_analysis"] })
         }
 

subworkflows/differential_expression.nf

@@ -76,6 +76,7 @@ process deAnalysis {
         path "de_analysis/results_dge.tsv", emit: dge
         path "de_analysis/results_dexseq.tsv", emit: dexseq
         path "de_analysis", emit: de_analysis
+        path "de_analysis/cpm_gene_counts.tsv", emit: cpm
     script:
     // Just try both annotation file type because a .gff extension may be gff2(gtf) or gff3
     String annotation_type = "gtf"
@@ -115,7 +116,15 @@ process plotResults {
     output:
         path "de_analysis/dtu_plots.pdf", emit: dtu_plots
         path "sample_sheet.tsv", emit: sample_sheet_csv
+        // Output all DE files for use in report process
         path "de_analysis/*", emit: stageR
+        // Output selected DE files to be output in out_dir
+        path "de_analysis/results_dge.pdf", emit: dge_pdf
+        path "de_analysis/results_dge.tsv", emit: dge_tsv
+        path "de_analysis/results_dtu_gene.tsv", emit: dtu_gene
+        path "de_analysis/results_dtu_transcript.tsv", emit: dtu_transcript
+        path "de_analysis/results_dtu_stageR.tsv", emit: dtu_stageR
+        path "de_analysis/results_dtu.pdf", emit: dtu_pdf
     """
     plot_dtu_results.R
     """
@@ -178,14 +187,18 @@ workflow differential_expression {
         merged_TPM = mergeTPM(count_transcripts.out.counts.collect())
         analysis = deAnalysis(sample_sheet, merged, ref_annotation)
         plotResults(analysis.flt_counts, analysis.stageR, sample_sheet, analysis.de_analysis)
+        // Concat files required for making the report
         de_report = analysis.flt_counts.concat(analysis.gene_counts, analysis.dge, analysis.dexseq,
         analysis.stageR, plotResults.out.sample_sheet_csv, merged, ref_annotation, merged_TPM, analysis.unflt_counts).collect()
+        // Concat files required to be output to user
+        de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, plotResults.out.dge_pdf, plotResults.out.dge_tsv,
+        plotResults.out.dtu_gene, plotResults.out.dtu_transcript, plotResults.out.dtu_stageR, plotResults.out.dtu_pdf).collect()
         count_transcripts_file = count_transcripts.out.seqkit_stats.collect()
         all_counts = merged_TPM.concat(analysis.flt_counts, analysis.gene_counts)
 emit:
        all_de = de_report
        count_transcripts = count_transcripts_file
        dtu_plots = plotResults.out.dtu_plots
-       de_outputs = plotResults.out.stageR
+       de_outputs = de_outputs_concat
        counts = all_counts
 }