Merge pull request #412 from nf-core/405-adding-depthcutoff-freyja

Add parameter freyja_depthcutoff

Author: Joon-Klaps

.devcontainer/devcontainer.json

@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }

CHANGELOG.md

@@ -20,16 +20,18 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[PR #387](https://github.com/nf-core/viralrecon/pull/387)] - Software closes gracefully when encountering an error
 - [[PR #395](https://github.com/nf-core/viralrecon/pull/395)] - Remove minia from default assemblers because it is unreliable
 - [[PR #393](https://github.com/nf-core/viralrecon/pull/393)] - Changed primer set to params
+- [[PR [#405](https://github.com/nf-core/viralrecon/issues/405)]] - Including parameter `depthcutoff` to freyja demix and boot
 
 ### Parameters
 
-| Old parameter       | New parameter |
-| ------------------- | ------------- |
-| `--skip_freyja`     |               |
-| `--freyja_repeats`  |               |
-| `--freyja_db_name`  |               |
-| `--freyja_barcodes` |               |
-| `--freyja_lineages` |               |
+| Old parameter          | New parameter |
+| ---------------------- | ------------- |
+| `--skip_freyja`        |               |
+| `--freyja_repeats`     |               |
+| `--freyja_db_name`     |               |
+| `--freyja_barcodes`    |               |
+| `--freyja_lineages`    |               |
+| `--freyja_depthcutoff` |               |
 
 > **NB:** Parameter has been **updated** if both old and new parameter information is present.
 > **NB:** Parameter has been **added** if just the new parameter information is present.

conf/modules_illumina.config

@@ -194,21 +194,28 @@ if (!params.skip_variants) {
     if (!params.skip_freyja) {
         process {
             withName: 'FREYJA_VARIANTS' {
+                ext.args = {}
                 publishDir = [
                     path: { "${params.outdir}/variants/freyja/variants" },
                     mode: params.publish_dir_mode,
                     pattern: "*.{tsv,csv}"
                 ]
             }
             withName: 'FREYJA_DEMIX' {
+                ext.args = [
+                    params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
+                ].join(' ').trim()
                 publishDir = [
                     path: { "${params.outdir}/variants/freyja/demix" },
                     mode: params.publish_dir_mode,
                     pattern: "*.{tsv,csv}"
                 ]
             }
             withName: 'FREYJA_BOOT' {
-                ext.args = '--boxplot pdf'
+                ext.args = [
+                    params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
+                    '--boxplot pdf',
+                ].join(' ').trim()
                 publishDir = [
                     path: { "${params.outdir}/variants/freyja/bootstrap" },
                     mode: params.publish_dir_mode,

conf/modules_nanopore.config

@@ -240,17 +240,23 @@ if (!params.skip_freyja) {
         }
 
         withName: 'FREYJA_DEMIX' {
+            ext.args = [
+                params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
+            ].join(' ').trim()
             publishDir = [
-                path: { "${params.outdir}/${params.artic_minion_caller}/freyja/demix" },
+                path: { "${params.outdir}/variants/freyja/demix" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{tsv,csv}"
             ]
         }
 
         withName: 'FREYJA_BOOT' {
-            ext.args = '--boxplot pdf'
+            ext.args = [
+                params.freyja_depthcutoff ? "--depthcutoff ${params.freyja_depthcutoff}" : '',
+                '--boxplot pdf',
+            ].join(' ').trim()
             publishDir = [
-                path: { "${params.outdir}/${params.artic_minion_caller}/freyja/bootstrap" },
+                path: { "${params.outdir}/variants/freyja/bootstrap" },
                 mode: params.publish_dir_mode,
                 pattern: "*.{tsv,csv,pdf}"
             ]

nextflow.config

@@ -43,6 +43,7 @@ params {
     max_multiqc_email_size     = '25.MB'
     skip_freyja                = false
     freyja_repeats             = 100
+    freyja_depthcutoff         = null
     freyja_db_name             = 'freyja_db'
     freyja_barcodes            = null
     freyja_lineages            = null

nextflow_schema.json

@@ -253,7 +253,7 @@
                 },
                 "skip_freyja": {
                     "type": "boolean",
-                    "fa_icon": "fas fast-forward",
+                    "fa_icon": "fas fa-forward",
                     "description": "Skip freyja deep SARS-CoV-2 variant analysis using a depth weighted approach."
                 },
                 "freyja_db_name": {
@@ -262,6 +262,12 @@
                     "fa_icon": "fas fa-folder-open",
                     "description": "Specify the name where to store UShER database (default: 'freyja_db')."
                 },
+                "freyja_depthcutoff": {
+                    "type": "number",
+                    "description": "Specify a coverage depth minimum which excludes sites with coverage less than the specified value",
+                    "fa_icon": "fas fa-hand-paper",
+                    "help_text": "Using the `depthcutoff` option may result in some distinct lineages now having identical barcodes, which are grouped into the format `[lineage]-like(num)` (based on their shared phylogeny) in the output."
+                },
                 "freyja_repeats": {
                     "type": "integer",
                     "default": 100,