[DRAFT] Add telseq "a software that estimates telomere length "

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller.
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
+- Added Telseq
 
 ### Changed
 

conf/modules/telseq.config

@@ -0,0 +1,28 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Config file for defining DSL2 per module options and publishing paths
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Available keys to override module options:
+        ext.args   = Additional arguments appended to command in module.
+        ext.args2  = Second set of arguments appended to command in module (multi-tool modules).
+        ext.args3  = Third set of arguments appended to command in module (multi-tool modules).
+        ext.prefix = File name prefix for output files.
+        ext.when   = When to run the module.
+----------------------------------------------------------------------------------------
+*/
+
+// TELSEQ
+
+process {
+    if (params.tools && params.tools.split(',').contains('telseq')) {
+
+        withName: 'TELSEQ' {
+            ext.when   = { params.tools && params.tools.split(',').contains('telseq') }
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/telseq/" },
+                pattern: "*.tsv"
+            ]
+        }
+    }
+}

docs/output.md

@@ -43,6 +43,8 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
       - [Sentieon Haplotyper joint germline variant calling](#sentieon-haplotyper-joint-germline-variant-calling)
     - [Lofreq](#lofreq)
     - [Strelka](#strelka)
+  - Telomeres
+    - [Telseq](#telseq)
   - [Structural Variants](#structural-variants)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
@@ -585,6 +587,22 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
   </details>
 
+### Telomeres
+
+#### Telseq
+
+[Telseq](https://github.com/zd1/telseq)  is a software that estimates telomere length from whole genome sequencing data.
+
+<details markdown = "1">
+<summary>Output files</summary>
+
+**Output directory: `{outdir}/telseq/`**
+
+-`<sample>.telseq.tsv`
+  - Telseq output
+  </details>
+
+
 ### Structural Variants
 
 #### Manta

docs/usage.md

@@ -585,6 +585,7 @@ This list is by no means exhaustive and it will depend on the specific analysis
 | [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
 | [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
+| [Telseq](https://github.com/zd1/telseq)                                                                 |  x  |  x  |   x    |    x    |   x   |    x    |
 | [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
 | [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |    -    |   -   |    x    |
 | [CNVKit](https://cnvkit.readthedocs.io/en/stable/)                                                      |  x  |  x  |   -    |    x    |   x   |    x    |