Merge branch 'dev' of github.com:nf-core/raredisease into modules_update

CHANGELOG.md

@@ -19,6 +19,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Installed the nf-core version of the sentieon/dedup module. The dedup module also contains a call to Sentieon's LocusCollector [#401](https://github.com/nf-core/raredisease/pull/401)
 - Removing Sentieon-based BQSR. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit [#402](https://github.com/nf-core/raredisease/pull/402)
 - Installed the nf-core version of the sentieon/dnamodelapply module [#403](https://github.com/nf-core/raredisease/pull/403)
+- Installed the nf-core version of the sentieon/wgsmetricsalgo module [#404](https://github.com/nf-core/raredisease/pull/404)
+- Installed the nf-core version of the sentieon/dnascope module [#406](https://github.com/nf-core/raredisease/pull/406)
 
 ### `Fixed`
 

conf/modules/align_sentieon.config

@@ -37,6 +37,7 @@ process {
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
         ext.args = { $params.rmdup ? "--rmdup" : '' }
         ext.prefix = { "${meta.id}_dedup" }
+        ext.suffix = ".bam"
         publishDir = [
             enabled: !params.save_mapped_as_cram,
             path: { "${params.outdir}/alignment" },

docs/usage.md

@@ -395,3 +395,24 @@ We recommend adding the following line to your environment to limit this (typica
 ```bash
 NXF_OPTS='-Xms1g -Xmx4g'
 ```
+
+### Running the pipeline without Internet access
+
+The pipeline and container images can be downloaded using [nf-core tools](https://nf-co.re/docs/usage/offline). For running offline, you of course have to make all the reference data available locally, and specify `--fasta`, etc., see [above](#reference-files-and-parameters).
+
+Contrary to the paragraph about [Nextflow](https://nf-co.re/docs/usage/offline#nextflow) on the page linked above, it is not possible to use the "-all" packaged version of Nextflow for this pipeline. The online version of Nextflow is necessary to support the necessary nextflow plugins. Download instead the file called just `nextflow`. Nextflow will download its dependencies when it is run. Additionally, you need to download the nf-validation plugin explicitly:
+
+```
+./nextflow plugin install nf-validation
+```
+
+Now you can transfer the `nextflow` binary as well as its directory `$HOME/.nextflow` to the system without Internet access, and use it there. It is necessary to use an explicit version of `nf-validation` offline, or Nextflow will check for the most recent version online. Find the version of nf-validation you downloaded in `$HOME/.nextflow/plugins`, then specify this version for `nf-validation` in your configuration file:
+
+```
+plugins {
+        // Set the plugin version explicitly, otherwise nextflow will look for the newest version online.
+        id '[email protected]'
+}
+```
+
+This should go in your Nextflow confgiguration file, specified with `-c <YOURCONFIG>` when running the pipeline.

modules.json

@@ -375,11 +375,21 @@
                         "git_sha": "43ef68091a1188fd8dc4c03f9341b556803c7514",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/dnascope": {
+                        "branch": "master",
+                        "git_sha": "127edadc279e19da093fdd513926c6cdee82c306",
+                        "installed_by": ["modules"]
+                    },
                     "sentieon/readwriter": {
                         "branch": "master",
                         "git_sha": "b28e4dde755117e8dab5d6e85e292f145b8b53c3",
                         "installed_by": ["modules"]
                     },
+                    "sentieon/wgsmetrics": {
+                        "branch": "master",
+                        "git_sha": "b1e9314b919f498e116bfc1417b7185185e99261",
+                        "installed_by": ["modules"]
+                    },
                     "smncopynumbercaller": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",