Merge branch 'CW-4886' into 'dev'

Tidy de analysis

Closes CW-4886

See merge request epi2melabs/workflows/wf-transcriptomes!185

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - If required for IGV, reference indexes are output in to a `igv_reference` directory
 ### Changed
 - BAMS are output in to a BAMS directory.
+- Reconcile with template 5.2.6.
 
 ## [v1.3.0]
 ### Removed

bin/de_analysis.R

@@ -9,13 +9,14 @@ min_samps_gene_expr <- as.numeric(args[2])
 min_samps_feature_expr <- as.numeric(args[3])
 min_gene_expr <- as.numeric(args[4]) 
 min_feature_expr <- as.numeric(args[5])
+sample_sheet <- args[6]
 
 cat("Loading counts, conditions and parameters.\n")
 cts <- as.matrix(read.csv("all_counts.tsv", sep="\t", row.names="Reference", stringsAsFactors=FALSE))
 
 # Set up sample data frame:
 #changed this to sample_id
-coldata <- read.csv("sample_sheet.csv", row.names="alias", sep=",", stringsAsFactors=TRUE)
+coldata <- read.csv(sample_sheet, row.names="alias", sep=",", stringsAsFactors=TRUE)
 
 coldata$sample_id <- rownames(coldata)
 # check if control condition exists, sets as reference 

main.nf

@@ -717,9 +717,7 @@ workflow pipeline {
             de = differential_expression(transcriptome, input_reads, sample_sheet, gtf)
             de_report = de.all_de
             count_transcripts_file = de.count_transcripts
-            dtu_plots = de.dtu_plots
             de_outputs = de.de_outputs
-            counts = de.counts
         } else{
             de_report = OPTIONAL_FILE
             count_transcripts_file = OPTIONAL_FILE
@@ -763,7 +761,7 @@ workflow pipeline {
 
         if (params.de_analysis){
            de_results = report.concat(
-            transcriptome, de_outputs.flatten(), counts.flatten(),
+            transcriptome, de_outputs.flatten(),
             makeReport.out.results_dge,  makeReport.out.tpm,
             makeReport.out.filtered,  makeReport.out.unfiltered,
             makeReport.out.gene_counts)

nextflow.config

@@ -21,7 +21,6 @@ params {
      // Thresholds for viewing isoforms in report table
     isoform_table_nrows = 5000
 
-
     out_dir = "output"
     sample = null
     sample_sheet = null
@@ -95,8 +94,8 @@ params {
         "--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
       ]
     agent = null
-    container_sha = "shafb1e2372e1535f0b42891ed2c68ffdac2ca1d658"
+    container_sha = "shad8671ea3a8ed52f2c0f40355e8eb5c6f00d2cbda"
-	common_sha = "shae58638742cf84dbeeec683ba24bcdee67f64b986"
+	common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
     }
 }
 

subworkflows/differential_expression.nf

@@ -69,16 +69,21 @@ process deAnalysis {
     output:
         path "de_analysis/results_dtu_stageR.tsv", emit: stageR
         path "merged/filtered_transcript_counts_with_genes.tsv", emit: flt_counts
-        path "de_analysis/unfiltered_transcript_counts_with_genes.tsv", emit: unflt_counts
         path "merged/all_gene_counts.tsv", emit: gene_counts
+        path "de_analysis/unfiltered_transcript_counts_with_genes.tsv", emit: unflt_counts
         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/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
         path "de_analysis/cpm_gene_counts.tsv", emit: cpm
     """
     mkdir merged
     mkdir de_analysis
-    de_analysis.R annotation.gtf $params.min_samps_gene_expr $params.min_samps_feature_expr $params.min_gene_expr $params.min_feature_expr
+    de_analysis.R annotation.gtf $params.min_samps_gene_expr $params.min_samps_feature_expr $params.min_gene_expr $params.min_feature_expr "sample_sheet.csv"
     """
 }
 
@@ -91,23 +96,10 @@ process plotResults {
         path "filtered_transcript_counts_with_genes.tsv"
         path "results_dtu_stageR.tsv"
         path "sample_sheet.tsv"
-        path de_analysis
     output:
-        path "de_analysis/dtu_plots.pdf", emit: dtu_plots
+        path "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
-    # output plots to common analysis output directory
-    cp dtu_plots.pdf de_analysis/dtu_plots.pdf
     """
 }
 
@@ -159,6 +151,7 @@ workflow differential_expression {
        sample_sheet
        ref_annotation
     main:
+        sample_sheet = Channel.fromPath(sample_sheet)
         checkSampleSheetCondition(sample_sheet)
         t_index = build_minimap_index_transcriptome(ref_transcriptome)
         mapped = map_transcriptome(full_len_reads.combine(t_index)
@@ -167,19 +160,16 @@ workflow differential_expression {
         merged = mergeCounts(count_transcripts.out.counts.collect())
         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)
+        plotResults(analysis.flt_counts, analysis.stageR, sample_sheet)
         // 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()
+        analysis.stageR, sample_sheet, merged, ref_annotation, merged_TPM, analysis.unflt_counts).collect()
-        // Concat files required to be output to user
+        // Concat files required to be output to user without any changes
-        de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, plotResults.out.dge_pdf, plotResults.out.dge_tsv,
+        de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, analysis.dge_pdf, analysis.dge_tsv,
-        plotResults.out.dtu_gene, plotResults.out.dtu_transcript, plotResults.out.dtu_stageR, plotResults.out.dtu_pdf).collect()
+        analysis.dtu_gene, analysis.dtu_transcript, analysis.dtu_stageR, analysis.dtu_pdf, analysis.flt_counts, analysis.gene_counts, merged_TPM).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 = de_outputs_concat
-       counts = all_counts
 }