feat(ribowaltz): Export underlying data from QC plots

modules/nf-core/ribowaltz/main.nf

@@ -22,6 +22,7 @@ process RIBOWALTZ {
     tuple val(meta), path("*.cds_coverage_psite.tsv{,.gz}")   , emit: cds_coverage         , optional: true
     tuple val(meta), path("*nt_coverage_psite.tsv{,.gz}")     , emit: cds_window_coverage  , optional: true
     tuple val(meta), path("ribowaltz_qc/*.pdf")               , emit: ribowaltz_qc         , optional: true
+    tuple val(meta), path("ribowaltz_qc/*.tsv")               , emit: ribowaltz_qc_data    , optional: true
     path "versions.yml"                                       , emit: versions
 
     when:
@@ -41,6 +42,9 @@ process RIBOWALTZ {
     touch ${prefix}.cds_coverage_psite.tsv
     mkdir -p offset_plot/${prefix} && touch offset_plot/${prefix}/29.pdf
     mkdir -p ribowaltz_qc && touch ribowaltz_qc/${prefix}.metaprofile_psite.pdf
+    touch ribowaltz_qc/${prefix}.psite_region.tsv
+    touch ribowaltz_qc/${prefix}.frames.tsv
+    touch ribowaltz_qc/${prefix}.frames_stratified.tsv
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/ribowaltz/meta.yml

@@ -164,6 +164,19 @@ output:
           description: riboWaltz diagnostic plots (optional)
           pattern: "ribowaltz_qc/*"
           ontologies: []
+  ribowaltz_qc_data:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - ribowaltz_qc/*.tsv:
+          type: file
+          description: TSV files containing data underlying riboWaltz QC plots including
+            P-site region distribution, frame distribution, and frame distribution
+            stratified by read length (optional)
+          pattern: "ribowaltz_qc/*.tsv"
+          ontologies: []
   versions:
     - versions.yml:
         type: file

modules/nf-core/ribowaltz/templates/ribowaltz.r

@@ -294,6 +294,11 @@ save_psite_region_plot <- function(sample_name, dt.ls, annotation.df) {
 
     ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".psite_region.pdf"), psite_region.gg, dpi = 400, width = 10)
 
+    # Export underlying data
+    region_dt <- psite_region[["count_dt"]]
+    if (!is.null(region_dt)) {
+        data.table::fwrite(region_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".psite_region.tsv"), sep = "\t")
+    }
 }
 
 #' Save Frame Plots
@@ -329,12 +334,22 @@ save_frame_plots <- function(sample_name, dt.ls, annotation.df, min_length, max_
 
     ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames_stratified.pdf"), frames_stratified.gg, dpi = 600, height = 9 , width = 12)
 
+    # Export underlying data for stratified frames
+    frames_stratified_dt <- frames_stratified[["count_dt"]]
+    if (!is.null(frames_stratified_dt)) {
+        data.table::fwrite(frames_stratified_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames_stratified.tsv"), sep = "\t")
+    }
 
     frames <- riboWaltz::frame_psite(dt.ls, region = "all", length_range = min_length:max_length, sample = sample_name, annotation = annotation.df, colour = "grey70")
     frames.gg <- frames[[paste0("plot_", sample_name)]]
 
     ggplot2::ggsave(paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames.pdf"), frames.gg, dpi = 600, height = 9 , width = 9)
 
+    # Export underlying data for aggregated frames
+    frames_dt <- frames[["count_dt"]]
+    if (!is.null(frames_dt)) {
+        data.table::fwrite(frames_dt, paste0(getwd(), "/ribowaltz_qc/", sample_name, ".frames.tsv"), sep = "\t")
+    }
 }
 
 

modules/nf-core/ribowaltz/tests/main.nf.test

@@ -36,6 +36,7 @@ nextflow_process {
                 { assert snapshot(process.out.cds_coverage).match('cds_coverage') },
                 { assert snapshot(process.out.cds_window_coverage).match('cds_window_coverage') },
                 { assert snapshot(process.out.ribowaltz_qc.size() == 8) },
+                { assert snapshot(process.out.ribowaltz_qc_data.size() == 3) },
                 { assert snapshot(process.out.versions).match('versions') }
             )
         }
@@ -69,6 +70,7 @@ nextflow_process {
                 { assert snapshot(process.out.codon_coverage_psite).match('codon_coverage_psite_stub') },
                 { assert snapshot(process.out.cds_coverage).match('cds_coverage_stub') },
                 { assert snapshot(process.out.ribowaltz_qc.size() == 1) },
+                { assert snapshot(process.out.ribowaltz_qc_data.size() == 3) },
                 { assert snapshot(process.out.versions).match('versions_stub') }
             )
         }