Emit both png and pdf plots in deseq2

modules/nf-core/deseq2/differential/main.nf

@@ -15,7 +15,8 @@ process DESEQ2_DIFFERENTIAL {
 
     output:
     tuple val(meta), path("*.deseq2.results.tsv")              , emit: results
-    tuple val(meta), path("*.deseq2.dispersion.png")           , emit: dispersion_plot
+    tuple val(meta), path("*.deseq2.dispersion.png")           , emit: dispersion_plot_png
+    tuple val(meta), path("*.deseq2.dispersion.pdf")           , emit: dispersion_plot_pdf
     tuple val(meta), path("*.dds.rld.rds")                     , emit: rdata
     tuple val(meta), path("*.deseq2.sizefactors.tsv")          , emit: size_factors
     tuple val(meta), path("*.normalised_counts.tsv")           , emit: normalised_counts
@@ -35,6 +36,7 @@ process DESEQ2_DIFFERENTIAL {
     """
     touch ${meta.id}.deseq2.results.tsv
     touch ${meta.id}.deseq2.dispersion.png
+    touch ${meta.id}.deseq2.dispersion.pdf
     touch ${meta.id}.dds.rld.rds
     touch ${meta.id}.deseq2.sizefactors.tsv
     touch ${meta.id}.normalised_counts.tsv

modules/nf-core/deseq2/differential/meta.yml

@@ -61,7 +61,7 @@ input:
           RNA-seq workflow
         ontologies: []
   - - meta3:
-        type: file
+        type: map
         description: |
           Meta map describing control genes, e.g. [ id: 'ERCC' ]
         ontologies: []
@@ -85,131 +85,115 @@ input:
 output:
   results:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.deseq2.results.tsv":
           type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
+          description: TSV-format table of differential expression information as output by DESeq2
+          pattern: "*.deseq2.results.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
-  dispersion_plot:
+  dispersion_plot_png:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.deseq2.dispersion.png":
           type: file
-          description: DESeq2 dispersion plot
-          pattern: "deseq2.dispersion.png"
-          ontologies: []
-  rdata:
+          description: DESeq2 dispersion plot in PNG format
+          pattern: "*.deseq2.dispersion.png"
+          ontologies:
+            - edam: "http://edamontology.org/format_3603" # PNG
+  dispersion_plot_pdf:
     - - meta:
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
+      - "*.deseq2.dispersion.pdf":
           type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
+          description: DESeq2 dispersion plot in PDF format
+          pattern: "*.deseq2.dispersion.pdf"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: "http://edamontology.org/format_3508" # PDF
+  rdata:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.dds.rld.rds":
           type: file
           description: Serialised DESeq2 object
-          pattern: "dds.rld.rds"
+          pattern: "*.dds.rld.rds"
           ontologies: []
   size_factors:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.deseq2.sizefactors.tsv":
           type: file
-          description: Size factors
-          pattern: "deseq2.sizefactors.tsv"
+          description: TSV-format table containing DESeq2 size factors
+          pattern: "*.deseq2.sizefactors.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
   normalised_counts:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.normalised_counts.tsv":
           type: file
           description: TSV-format counts matrix, normalised to size factors
-          pattern: "normalised_counts.tsv"
+          pattern: "*.normalised_counts.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
   rlog_counts:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.rlog.tsv":
           type: file
           description: |
             Optional, TSV-format counts matrix, normalised to size factors, with
             variance stabilisation applied via `rlog()`.
-          pattern: "rlog.tsv"
+          pattern: "*.rlog.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
   vst_counts:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.vst.tsv":
           type: file
           description: |
             Optional, TSV-format counts matrix, normalised to size factors, with
             variance stabilisation applied via `vst()`.
-          pattern: "vst_counts.tsv"
+          pattern: "*.vst.tsv"
           ontologies:
             - edam: http://edamontology.org/format_3475 # TSV
   model:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.deseq2.model.txt":
           type: file
           description: TXT-format DESeq2 model
-          pattern: "deseq2.model.tsv"
+          pattern: "*.deseq2.model.txt"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_2330 # TXT
   session_info:
     - - meta:
-          type: file
-          description: TSV-format table of differential expression information as output
-            by DESeq2
-          pattern: "deseq2.results.tsv"
-          ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+          type: map
+          description: |
+            Groovy Map containing contrast information, same as input meta
       - "*.R_sessionInfo.log":
           type: file
-          description: dump of R SessionInfo
-          pattern: "*.log"
+          description: Dump of R SessionInfo
+          pattern: "*.R_sessionInfo.log"
           ontologies: []
   versions:
     - versions.yml:

modules/nf-core/deseq2/differential/templates/deseq2_differential.R

@@ -512,6 +512,12 @@ png(
 plotDispEsts(dds)
 dev.off()
 
+pdf(
+  file = paste(opt\$output_prefix, 'deseq2.dispersion.pdf', sep = '.')
+)
+plotDispEsts(dds)
+dev.off()
+
 # R object for other processes to use
 
 saveRDS(dds, file = paste(opt\$output_prefix, 'dds.rld.rds', sep = '.'))

modules/nf-core/deseq2/differential/tests/main.nf.test

@@ -49,7 +49,8 @@ nextflow_process {
                         process.out.vst_counts,
                         process.out.model,
                         process.out.versions,
-                        file(process.out.dispersion_plot[0][1]).name,
+                        file(process.out.dispersion_plot_png[0][1]).name,
+                        file(process.out.dispersion_plot_pdf[0][1]).name,
                         file(process.out.rdata[0][1]).name
                     ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -97,7 +98,8 @@ nextflow_process {
                         process.out.vst_counts,
                         process.out.model,
                         process.out.versions,
-                        file(process.out.dispersion_plot[0][1]).name,
+                        file(process.out.dispersion_plot_png[0][1]).name,
+                        file(process.out.dispersion_plot_pdf[0][1]).name,
                         file(process.out.rdata[0][1]).name
                     ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -145,7 +147,8 @@ nextflow_process {
                         process.out.vst_counts,
                         process.out.model,
                         process.out.versions,
-                        file(process.out.dispersion_plot[0][1]).name,
+                        file(process.out.dispersion_plot_png[0][1]).name,
+                        file(process.out.dispersion_plot_pdf[0][1]).name,
                         file(process.out.rdata[0][1]).name
                     ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -193,7 +196,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -246,7 +250,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -295,7 +300,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -346,7 +352,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -397,7 +404,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -451,7 +459,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -499,7 +508,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -547,7 +557,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -595,7 +606,8 @@ nextflow_process {
                     process.out.vst_counts,
                     process.out.model,
                     process.out.versions,
-                    file(process.out.dispersion_plot[0][1]).name,
+                    file(process.out.dispersion_plot_png[0][1]).name,
+                    file(process.out.dispersion_plot_pdf[0][1]).name,
                     file(process.out.rdata[0][1]).name
                 ).match() },
                 { assert path(process.out.session_info[0][1]).text.contains("DESeq2_1.34.0") }
@@ -636,7 +648,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot( process.out).match() }
+                { assert snapshot( process.out ).match() }
             )
         }
     }