Make MAD plots optional in shinyngs (#3334)

* Make MAD plots optional in shinyngs

* Fix types for linting

* fix other meta.ymls

* Add keywords

* file to tuple

* Hopefully final meta corrections

modules/nf-core/shinyngs/app/meta.yml

@@ -34,15 +34,15 @@ input:
       description: |
         TSV-format feature (e.g. gene) metadata
   - assay_files:
-      type: list
+      type: file
       description: |
         List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).
   - contrasts:
       type: file
       description: |
         CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors.
   - differential_results:
-      type: list
+      type: file
       description: |
         List of TSV-format differential analysis outputs, one per row of the contrasts file
 

modules/nf-core/shinyngs/staticdifferential/meta.yml

@@ -27,7 +27,7 @@ input:
         features and samples, at a minimum an id.
         e.g. [ id:'test' ]
   - differential_results:
-      type: list
+      type: file
       description: |
         CSV or TSV-format tabular file with differential analysis outputs
   - sample:
@@ -39,7 +39,7 @@ input:
       description: |
         CSV or TSV-format feature (e.g. gene) metadata
   - assay_file:
-      type: list
+      type: file
       description: |
         CSV or TSV matrix file to use alongside differential statistics in
         interpretation. Usually a normalised form.
@@ -50,11 +50,16 @@ output:
       description: |
         Groovy Map containing contrast information
         e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ]
-  - volcanos:
-      type: tuple
+  - volcanos_png:
+      type: file
+      description: |
+        Meta-keyed tuple containing a PNG output for a volcano plot built from
+        the differential result table.
+  - volcanos_html:
+      type: file
       description: |
-        Meta-keyed tuple containing a PNG and HTML plot for a volcano plot
-        built from the differential result table.
+        Meta-keyed tuple containing an HTML output for a volcano plot built
+        from the differential result table.
   - versions:
       type: file
       description: File containing software versions

modules/nf-core/shinyngs/staticexploratory/main.nf

@@ -19,7 +19,7 @@ process SHINYNGS_STATICEXPLORATORY {
     tuple val(meta), path("*/html/pca2d.html")                  , emit: pca2d_html, optional: true
     tuple val(meta), path("*/png/pca3d.png")                    , emit: pca3d_png
     tuple val(meta), path("*/html/pca3d.html")                  , emit: pca3d_html, optional: true
-    tuple val(meta), path("*/png/mad_correlation.png")          , emit: mad_png
+    tuple val(meta), path("*/png/mad_correlation.png")          , emit: mad_png, optional: true
     tuple val(meta), path("*/html/mad_correlation.html")        , emit: mad_html, optional: true
     tuple val(meta), path("*/png/sample_dendrogram.png")        , emit: dendro
     path "versions.yml"                                         , emit: versions

modules/nf-core/shinyngs/staticexploratory/meta.yml

@@ -30,40 +30,64 @@ input:
       description: |
         TSV-format feature (e.g. gene) metadata
   - assay_files:
-      type: list
+      type: file
       description: |
         List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).
 output:
-  - boxplots:
-      type: tuple
+  - boxplots_png:
+      type: file
+      description: |
+        Meta-keyed tuple containing PNG output for box plots covering input
+        matrices.
+  - boxplots_html:
+      type: file
+      description: |
+        Meta-keyed tuple containing HTML output for box plots covering input
+        matrices.
+  - densities_png:
+      type: file
       description: |
-        Meta-keyed tuple containing a PNG and HTML output for box plots
+        Meta-keyed tuple containing PNG output for density plots
         covering input matrices.
-  - densities:
-      type: tuple
+  - densities_html:
+      type: file
       description: |
-        Meta-keyed tuple containing a PNG and HTML output for density plots
+        Meta-keyed tuple containing HTML output for density plots
         covering input matrices.
-  - pca2d:
-      type: tuple
+  - pca2d_png:
+      type: file
+      description: |
+        Meta-keyed tuple containing a PNG output for 2D PCA plots covering
+        specified input matrix (by default the last one in the input list.
+  - pca2d_html:
+      type: file
       description: |
-        Meta-keyed tuple containing a PNG and HTML plot for 2D PCA plots
+        Meta-keyed tuple containing an HTML output for 2D PCA plots covering
+        specified input matrix (by default the last one in the input list.
+  - pca3d_png:
+      type: file
+      description: |
+        Meta-keyed tuple containing a PNG output for 3D PCA plots covering
+        specified input matrix (by default the last one in the input list.
+  - pca3d_html:
+      type: file
+      description: |
+        Meta-keyed tuple containing an HTML output for 3D PCA plots covering
+        specified input matrix (by default the last one in the input list.
+  - mad_png:
+      type: file
+      description: |
+        Meta-keyed tuple containing a PNG output for MAD correlation plots
         covering specified input matrix (by default the last one in the input
         list.
-  - pca3d:
-      type: tuple
+  - mad_dendro:
+      type: file
       description: |
-        Meta-keyed tuple containing a PNG and HTML plot for 3D PCA plots
+        Meta-keyed tuple containing an HTML output for MAD correlation plots
         covering specified input matrix (by default the last one in the input
         list.
-  - mad:
-      type: tuple
-      description: |
-        Meta-keyed tuple containing a PNG and  HTML plot for MAD correlation
-        plots covering specified input matrix (by default the last one in the
-        input list.
   - dendro:
-      type: tuple
+      type: file
       description: |
         Meta-keyed tuple containing a PNG, for a sample clustering
         dendrogramcovering specified input matrix (by default the last one in

modules/nf-core/shinyngs/validatefomcomponents/meta.yml

@@ -3,6 +3,9 @@ description: validate consistency of feature and sample annotations with matrice
 
 keywords:
   - expression
+  - features
+  - observations
+  - validation
 
 tools:
   - "shinyngs":
@@ -42,7 +45,7 @@ input:
       description: |
         TSV-format feature (e.g. gene) metadata
   - assay_files:
-      type: list
+      type: file
       description: |
         List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised).
   - contrasts: