Add TPM the quantification RDS

nf-core · May 10, 2024 · 86af7b2 · 86af7b2
1 parent dbc4042
commit 86af7b2
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Showing 3 changed files with 8 additions and 2 deletions.
diff --git a/modules/local/quantification/merge_experiments/main.nf b/modules/local/quantification/merge_experiments/main.nf
@@ -8,9 +8,10 @@ process MERGE_EXPERIMENTS {
         'biocontainers/bioconductor-rtracklayer:1.62.0--r43ha9d7317_0' }"
 
     input:
-    tuple val(meta), path(experiments)
+    tuple val(meta),  path(experiments)
     tuple val(meta2), path(phenotype)
     tuple val(meta3), path(gtf)
+    tuple val(meta4), path(tpm)
 
     output:
     tuple val(meta), path("${meta.id}.merged.rds"), emit: merged

diff --git a/modules/local/quantification/merge_experiments/templates/merge_experiments.r b/modules/local/quantification/merge_experiments/templates/merge_experiments.r
@@ -7,6 +7,7 @@ experiments <- lapply(paths, readRDS)
 
 phenotype <- read.csv('${phenotype}', stringsAsFactors = FALSE)
 annotation <- rtracklayer::import('${gtf}')
+tpm <- read.table('${tpm}', header=TRUE, row.names=1)[, -1]
 
 se_assays <- list()
 
@@ -42,6 +43,9 @@ for (col in colnames(colData(se))) {
 annotation <- annotation[match(rownames(se), annotation\$transcript_id),]
 rowData(se) <- annotation
 
+# Add TPM
+assay(se, "tpm", withDimnames = FALSE) <- tpm[rownames(se), colData(se)\$names]
+
 saveRDS(se, '${meta.id}.merged.rds')
 
 writeLines(

diff --git a/subworkflows/local/quantification.nf b/subworkflows/local/quantification.nf
@@ -106,7 +106,8 @@ workflow QUANTIFICATION {
     MERGE_EXPERIMENTS(
         TXIMETA_TXIMETA.out.se.map{meta, se -> se}.collect().map{[[id: "experiments"], it]},
         ch_phenotype,
-        EXCLUDE_OVERLONG_TRANSCRIPTS.out.output
+        EXCLUDE_OVERLONG_TRANSCRIPTS.out.output,
+        JOIN_TX_TPM.out.csv
     )
 
     ch_versions = ch_versions.mix(