Apply suggestions from code review

genomic-medicine-sweden · Aug 26, 2024 · 20f9d4b · 20f9d4b
1 parent 20580e5
commit 20f9d4b
Show file tree

Hide file tree

Showing 3 changed files with 19 additions and 9 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -196,17 +196,21 @@ The mandatory and optional parameters for each category are tabulated below.
 
 #### 5. SNV annotation (ensembl VEP)
 
-| Mandatory | Optional                      |
-| --------- | ----------------------------- |
-|           | skip_vep<sup>1</sup>          |
-|           | vep_plugin_files<sup>2</sup>  |
-|           | vep_cache<sup>2</sup>         |
-|           | vep_cache_version<sup>3</sup> |
-|           | gene_panel_clinical_filter    |
+| Mandatory | Optional                         |
+| --------- | -------------------------------- |
+|           | skip_vep<sup>1</sup>             |
+|           | vep_plugin_files<sup>2</sup>     |
+|           | vep_cache<sup>2</sup>            |
+|           | vep_cache_version<sup>3</sup>    |
+|           | skip_download_vep<sup>4</sup>    |
+|           | skip_download_gnomad<sup>4</sup> |
+|           | vep_refs_download                |
+|           | gene_panel_clinical_filter       |
 
 <sup>1</sup> If it is not provided by the user, the default value is false<br />
 <sup>2</sup> VEP cache and plugins can be automatically downloaded by the pipeline by setting `--skip_download_vep false`, `--skip_download_gnomad false` and providing a lcsv with a list of files to download `--vep_refs_download` as done [here](https://github.com/genomic-medicine-sweden/tomte/blob/dev/test_data/vep_to_download.csv). VEP caches can also be downloaded [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache). VEP plugins may also be installed in the cache directory, and the plugin pLI is mandatory to install. To supply files required by VEP plugins, use `vep_plugin_files` parameter. See example cache [here](https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz).<br />
 <sup>3</sup> If it is not provided by the user, the default value is 110, supported values are 107 and 110
+<sup>4</sup> If it is not provided by the user, the default value true
 
 #### 6. Stringtie & gffcompare
 

diff --git a/modules/local/vep_gnomad_download.nf b/modules/local/vep_gnomad_download.nf
@@ -43,8 +43,8 @@ process VEP_GNOMAD_DOWNLOAD {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         wget: \$(echo wget -V 2>&1 | grep "GNU Wget" | cut -d" " -f3 > versions.yml)
-         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
-         tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -233,6 +233,7 @@
                 },
                 "skip_downsample": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip downsampling before expression/splicing analysis. The number of reads to be used is defined by num_reads.",
                     "fa_icon": "fas fa-toggle-off"
                 },
@@ -281,26 +282,31 @@
                 },
                 "skip_build_tracks": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip building splice junction tracks for IGV.",
                     "fa_icon": "fas fa-toggle-off"
                 },
                 "skip_stringtie": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip analysis with StringTie",
                     "fa_icon": "fas fa-toggle-off"
                 },
                 "skip_vep": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip Ensembl Variant Effect Predictor",
                     "fa_icon": "fas fa-toggle-off"
                 },
                 "skip_drop_ae": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip DROP Aberrant Expression module ",
                     "fa_icon": "fas fa-toggle-off"
                 },
                 "skip_drop_as": {
                     "type": "boolean",
+                    "default": false,
                     "description": "Skip DROP Aberrant Splicing module",
                     "fa_icon": "fas fa-toggle-off"
                 },