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Fix links to docs #1328

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merged 3 commits into from
Nov 14, 2023
Merged

Fix links to docs #1328

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0834131
add icons + fix link
maxulysse Nov 14, 2023
02ef5c5
fix link
maxulysse Nov 14, 2023
a2db8d0
update CHANGELOG
maxulysse Nov 14, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion docs/output.md
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Expand Up @@ -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

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4 changes: 3 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -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",
Expand Down Expand Up @@ -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"
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