Switch deseq2_vst to true by default

Author: drpatelh

docs/output.md

@@ -261,7 +261,7 @@ The [featureCounts](http://bioinf.wehi.edu.au/featureCounts/) tool is used to co
 
 **This pipeline uses a standardised DESeq2 analysis script to get an idea of the reproducibility within the experiment, and to assess the overall differential binding. Please note that this will not suit every experimental design, and if there are other problems with the experiment then it may not work as well as expected.**
 
-For larger experiments, it may be recommended to use the `vst` transformation instead of the default `rlog` option. You can do this by providing the `--deseq2_vst` parameter to the pipeline. See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization) for a more detailed explanation.
+For larger experiments, it is recommended to use the `vst` transformation instead of the default `rlog` option. This is the default behaviour and can be controlled with the `--deseq2_vst` parameter. See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization) for a more detailed explanation.
 
 ![MultiQC - DESeq2 PCA plot](images/mqc_deseq2_pca_plot.png)
 

nextflow.config

@@ -50,7 +50,7 @@ params {
     skip_consensus_peaks       = false
 
     // Options: DESeq2 QC
-    deseq2_vst                 = false
+    deseq2_vst                 = true
     skip_deseq2_qc             = false
 
     // Options: QC

nextflow_schema.json

@@ -10,7 +10,9 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
+            "required": [
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -37,7 +39,13 @@
                     "type": "integer",
                     "description": "Read length used to calculate MACS2 genome size for peak calling if `--macs_gsize` isn't provided.",
                     "fa_icon": "fas fa-chart-area",
-                    "enum": [50, 75, 100, 150, 200]
+                    "enum": [
+                        50,
+                        75,
+                        100,
+                        150,
+                        200
+                    ]
                 },
                 "outdir": {
                     "type": "string",
@@ -221,7 +229,12 @@
                     "default": "bwa",
                     "description": "Specifies the alignment algorithm to use - available options are 'bwa', 'bowtie2' and 'star'.",
                     "fa_icon": "fas fa-map-signs",
-                    "enum": ["bwa", "bowtie2", "chromap", "star"]
+                    "enum": [
+                        "bwa",
+                        "bowtie2",
+                        "chromap",
+                        "star"
+                    ]
                 },
                 "keep_dups": {
                     "type": "boolean",
@@ -348,7 +361,8 @@
                     "type": "boolean",
                     "description": "Use vst transformation instead of rlog with DESeq2.",
                     "help_text": "See [DESeq2 docs](http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-transformations-and-visualization).",
-                    "fa_icon": "fas fa-dolly"
+                    "fa_icon": "fas fa-dolly",
+                    "default": true
                 },
                 "skip_plot_profile": {
                     "type": "boolean",
@@ -489,7 +503,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "fingerprint_bins": {