Merge branch 'CW-4886' into 'dev'
Tidy de analysis Closes CW-4886 See merge request epi2melabs/workflows/wf-transcriptomes!185
This commit is contained in:
Sarah Griffiths
commit
d2ddad27a2
@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- If required for IGV, reference indexes are output in to a `igv_reference` directory
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### Changed
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- BAMS are output in to a BAMS directory.
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- Reconcile with template 5.2.6.
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## [v1.3.0]
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### Removed
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@ -9,13 +9,14 @@ min_samps_gene_expr <- as.numeric(args[2])
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min_samps_feature_expr <- as.numeric(args[3])
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min_gene_expr <- as.numeric(args[4])
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min_feature_expr <- as.numeric(args[5])
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sample_sheet <- args[6]
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cat("Loading counts, conditions and parameters.\n")
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cts <- as.matrix(read.csv("all_counts.tsv", sep="\t", row.names="Reference", stringsAsFactors=FALSE))
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# Set up sample data frame:
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#changed this to sample_id
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coldata <- read.csv("sample_sheet.csv", row.names="alias", sep=",", stringsAsFactors=TRUE)
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coldata <- read.csv(sample_sheet, row.names="alias", sep=",", stringsAsFactors=TRUE)
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coldata$sample_id <- rownames(coldata)
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# check if control condition exists, sets as reference
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4
main.nf
4
main.nf
@ -717,9 +717,7 @@ workflow pipeline {
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de = differential_expression(transcriptome, input_reads, sample_sheet, gtf)
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de_report = de.all_de
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count_transcripts_file = de.count_transcripts
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dtu_plots = de.dtu_plots
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de_outputs = de.de_outputs
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counts = de.counts
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} else{
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de_report = OPTIONAL_FILE
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count_transcripts_file = OPTIONAL_FILE
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@ -763,7 +761,7 @@ workflow pipeline {
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if (params.de_analysis){
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de_results = report.concat(
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transcriptome, de_outputs.flatten(), counts.flatten(),
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transcriptome, de_outputs.flatten(),
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makeReport.out.results_dge, makeReport.out.tpm,
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makeReport.out.filtered, makeReport.out.unfiltered,
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makeReport.out.gene_counts)
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@ -21,7 +21,6 @@ params {
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// Thresholds for viewing isoforms in report table
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isoform_table_nrows = 5000
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out_dir = "output"
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sample = null
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sample_sheet = null
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@ -95,8 +94,8 @@ params {
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"--sample_sheet 'wf-transcriptomes-demo/sample_sheet.csv'",
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]
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agent = null
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container_sha = "shafb1e2372e1535f0b42891ed2c68ffdac2ca1d658"
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common_sha = "shae58638742cf84dbeeec683ba24bcdee67f64b986"
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container_sha = "shad8671ea3a8ed52f2c0f40355e8eb5c6f00d2cbda"
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common_sha = "shad28e55140f75a68f59bbecc74e880aeab16ab158"
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}
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}
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@ -69,16 +69,21 @@ process deAnalysis {
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output:
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path "de_analysis/results_dtu_stageR.tsv", emit: stageR
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path "merged/filtered_transcript_counts_with_genes.tsv", emit: flt_counts
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path "de_analysis/unfiltered_transcript_counts_with_genes.tsv", emit: unflt_counts
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path "merged/all_gene_counts.tsv", emit: gene_counts
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path "de_analysis/unfiltered_transcript_counts_with_genes.tsv", emit: unflt_counts
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path "de_analysis/results_dge.tsv", emit: dge
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path "de_analysis/results_dexseq.tsv", emit: dexseq
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path "de_analysis", emit: de_analysis
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path "de_analysis/results_dge.pdf", emit: dge_pdf
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path "de_analysis/results_dge.tsv", emit: dge_tsv
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path "de_analysis/results_dtu_gene.tsv", emit: dtu_gene
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path "de_analysis/results_dtu_transcript.tsv", emit: dtu_transcript
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path "de_analysis/results_dtu_stageR.tsv", emit: dtu_stageR
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path "de_analysis/results_dtu.pdf", emit: dtu_pdf
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path "de_analysis/cpm_gene_counts.tsv", emit: cpm
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"""
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mkdir merged
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mkdir de_analysis
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de_analysis.R annotation.gtf $params.min_samps_gene_expr $params.min_samps_feature_expr $params.min_gene_expr $params.min_feature_expr
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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"
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"""
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}
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@ -91,23 +96,10 @@ process plotResults {
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path "filtered_transcript_counts_with_genes.tsv"
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path "results_dtu_stageR.tsv"
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path "sample_sheet.tsv"
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path de_analysis
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output:
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path "de_analysis/dtu_plots.pdf", emit: dtu_plots
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path "sample_sheet.tsv", emit: sample_sheet_csv
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// Output all DE files for use in report process
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path "de_analysis/*", emit: stageR
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// Output selected DE files to be output in out_dir
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path "de_analysis/results_dge.pdf", emit: dge_pdf
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path "de_analysis/results_dge.tsv", emit: dge_tsv
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path "de_analysis/results_dtu_gene.tsv", emit: dtu_gene
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path "de_analysis/results_dtu_transcript.tsv", emit: dtu_transcript
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path "de_analysis/results_dtu_stageR.tsv", emit: dtu_stageR
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path "de_analysis/results_dtu.pdf", emit: dtu_pdf
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path "dtu_plots.pdf", emit: dtu_plots
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"""
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plot_dtu_results.R
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# output plots to common analysis output directory
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cp dtu_plots.pdf de_analysis/dtu_plots.pdf
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"""
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}
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@ -159,6 +151,7 @@ workflow differential_expression {
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sample_sheet
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ref_annotation
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main:
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sample_sheet = Channel.fromPath(sample_sheet)
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checkSampleSheetCondition(sample_sheet)
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t_index = build_minimap_index_transcriptome(ref_transcriptome)
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mapped = map_transcriptome(full_len_reads.combine(t_index)
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@ -167,19 +160,16 @@ workflow differential_expression {
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merged = mergeCounts(count_transcripts.out.counts.collect())
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merged_TPM = mergeTPM(count_transcripts.out.counts.collect())
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analysis = deAnalysis(sample_sheet, merged, ref_annotation)
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plotResults(analysis.flt_counts, analysis.stageR, sample_sheet, analysis.de_analysis)
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plotResults(analysis.flt_counts, analysis.stageR, sample_sheet)
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// Concat files required for making the report
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de_report = analysis.flt_counts.concat(analysis.gene_counts, analysis.dge, analysis.dexseq,
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analysis.stageR, plotResults.out.sample_sheet_csv, merged, ref_annotation, merged_TPM, analysis.unflt_counts).collect()
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// Concat files required to be output to user
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de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, plotResults.out.dge_pdf, plotResults.out.dge_tsv,
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plotResults.out.dtu_gene, plotResults.out.dtu_transcript, plotResults.out.dtu_stageR, plotResults.out.dtu_pdf).collect()
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analysis.stageR, sample_sheet, merged, ref_annotation, merged_TPM, analysis.unflt_counts).collect()
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// Concat files required to be output to user without any changes
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de_outputs_concat = analysis.cpm.concat(plotResults.out.dtu_plots, analysis.dge_pdf, analysis.dge_tsv,
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analysis.dtu_gene, analysis.dtu_transcript, analysis.dtu_stageR, analysis.dtu_pdf, analysis.flt_counts, analysis.gene_counts, merged_TPM).collect()
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count_transcripts_file = count_transcripts.out.seqkit_stats.collect()
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all_counts = merged_TPM.concat(analysis.flt_counts, analysis.gene_counts)
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emit:
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all_de = de_report
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count_transcripts = count_transcripts_file
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dtu_plots = plotResults.out.dtu_plots
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de_outputs = de_outputs_concat
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counts = all_counts
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}
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