Merge pull request #1328 from maxulysse/docs

Fix links to docs

CHANGELOG.md

@@ -39,6 +39,8 @@ Pårtetjåkko is a mountain in the south of the park.
 - [#1318](https://github.com/nf-core/sarek/pull/1218) - Fix writing of params.json on S3
 - [#1324](https://github.com/nf-core/sarek/pull/1324) - Fix various typos & code formatting
 - [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files
+- [#1328](https://github.com/nf-core/sarek/pull/1328) - Fix links to docs in `nextflow_schema.json` and `docs/output.md`
+- [#1328](https://github.com/nf-core/sarek/pull/1328) - Add missing icons in `nextflow_schema.json`
 
 ### Removed
 

docs/output.md

@@ -315,7 +315,7 @@ If some results from a variant caller do not appear here, please check out the `
 
 ### SNVs and small indels
 
-For single nucleotide variants (SNVs) and small indels, multiple tools are available for normal (germline), tumor-only, and tumor-normal (somatic) paired data. For a list of the appropriate tool(s) for the data and sequencing type at hand, please check [here](usage.md#which-tool).
+For single nucleotide variants (SNVs) and small indels, multiple tools are available for normal (germline), tumor-only, and tumor-normal (somatic) paired data. For a list of the appropriate tool(s) for the data and sequencing type at hand, please check [here](usage#which-tool).
 
 #### bcftools
 

nextflow_schema.json

@@ -27,6 +27,7 @@
                 "input_restart": {
                     "type": "string",
                     "description": "Automatic retrieval for restart",
+                    "fa_icon": "fas fa-file-csv",
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/csv",
@@ -176,11 +177,12 @@
                     "type": "string",
                     "fa_icon": "fas fa-tape",
                     "description": "Specify UMI read structure",
-                    "help_text": "One structure if UMI is present on one end (i.e. '+T 2M11S+T'), or two structures separated by a blank space if UMIs a present on both ends (i.e. '2M11S+T 2M11S+T'); please note, this does not handle duplex-UMIs.\n\nFor more info on UMI usage in the pipeline, also check docs [here](./docs/usage.md/#how-to-handle-umis)."
+                    "help_text": "One structure if UMI is present on one end (i.e. '+T 2M11S+T'), or two structures separated by a blank space if UMIs a present on both ends (i.e. '2M11S+T 2M11S+T'); please note, this does not handle duplex-UMIs.\n\nFor more info on UMI usage in the pipeline, also check docs [here](./docs/usage/#how-to-handle-umis)."
                 },
                 "group_by_umi_strategy": {
                     "type": "string",
                     "default": "Adjacency",
+                    "fa_icon": "fas fa-tape",
                     "description": "Default strategy with UMI",
                     "hidden": true,
                     "help_text": "Available values: Identity, Edit, Adjacency, Paired"