Merge pull request #203 from nf-cmgg/dev

Release PR v1.8.2
nf-cmgg · Sep 30, 2024 · b637c64 · b637c64
2 parents aef8a80 + 5bb62c6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,13 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v1.8.2 - Outstanding Oostkamp - [September 30 2024]
+
+## Fixes
+
+1. Fixed some issues where indices were not created
+2. Updated the docs
+
 ## v1.8.1 - Open Oostkamp - [September 25 2024]
 
 ### Fixes

diff --git a/docs/parameters.md b/docs/parameters.md
diff --git a/docs/usage.md b/docs/usage.md
@@ -12,6 +12,17 @@ You will need to create a samplesheet with information with the samples you woul
 --input '[path to samplesheet file]'
 ```
 
+### Watch for files in a directory
+
+When the `--watchdir` parameter has been given, the pipeline will automatically check for all files in the samplesheet that have the `watch:` prefix in the given directory. An example for watching CRAM files:
+
+```csv title="samplesheet.csv"
+sample,cram,crai
+SAMPLE_1,watch:INPUT.cram,watch:INPUT.cram.crai
+```
+
+The files `INPUT.cram` and `INPUT.cram.crai` will now watched for recursively in the watch directory.
+
 ### Example of the samplesheet
 
 Below is an example of how the samplesheet could look like in the three formats.

diff --git a/modules.json b/modules.json
@@ -13,7 +13,7 @@
                     },
                     "bcftools/concat": {
                         "branch": "master",
-                        "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890",
+                        "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                         "installed_by": ["vcf_annotate_ensemblvep_snpeff"]
                     },
                     "bcftools/filter": {

diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf
diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml
diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test