Add depthcutoff parameter of FREYJA_BOOT and FREYJA_DEMIX modules as …

…freyja_depthcutoff
nf-core · Jan 17, 2024 · 24b0952 · 24b0952
1 parent ce72f48
commit 24b0952
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Showing 4 changed files with 25 additions and 5 deletions.
diff --git a/conf/modules_illumina.config b/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,

diff --git a/conf/modules_nanopore.config b/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}"
             ]

diff --git a/nextflow.config b/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

diff --git a/nextflow_schema.json b/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,