From aa66a9456c5cfe1eb414fb4f7b5a6c446ab59de5 Mon Sep 17 00:00:00 2001
From: Samuel Lampa <samuel.lampa@scilifelab.se>
Date: Wed, 29 Jan 2025 13:34:22 +0100
Subject: [PATCH] Run nf-core pipelines schema build to format schema file

---
 nextflow_schema.json | 49 ++++++++++++++++++++++++++++++++++++--------
 1 file changed, 41 insertions(+), 8 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 0ed86f81..007ce671 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -82,7 +82,9 @@
                     "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
                 }
             },
-            "required": ["outdir"],
+            "required": [
+                "outdir"
+            ],
             "fa_icon": "fas fa-terminal"
         },
         "sequencing_input": {
@@ -259,7 +261,11 @@
                     "default": "independent",
                     "help_text": "If samples are treated independent (lowest sensitivity and lowest resources), pooled (highest sensitivity and resources) or pseudo-pooled (balance between required resources and sensitivity).",
                     "description": "Mode of sample inference: \"independent\", \"pooled\" or \"pseudo\"",
-                    "enum": ["independent", "pooled", "pseudo"]
+                    "enum": [
+                        "independent",
+                        "pooled",
+                        "pseudo"
+                    ]
                 },
                 "concatenate_reads": {
                     "type": "boolean",
@@ -438,7 +444,10 @@
                     "type": "string",
                     "description": "Method used for alignment, \"hmmer\" or \"mafft\"",
                     "default": "hmmer",
-                    "enum": ["hmmer", "mafft"]
+                    "enum": [
+                        "hmmer",
+                        "mafft"
+                    ]
                 },
                 "pplace_taxonomy": {
                     "type": "string",
@@ -454,7 +463,13 @@
                     "type": "string",
                     "help_text": "Choose any of the supported databases, and optionally also specify the version. Database and version are separated by an equal sign (`=`, e.g. `silva=138`) . This will download the desired database and initiate taxonomic classification with QIIME2 and the chosen database.\n\nIf both, `--dada_ref_taxonomy` and `--qiime_ref_taxonomy` are used, DADA2 classification will be used for downstream analysis.\n\nThe following databases are supported:\n- SILVA ribosomal RNA gene database project - 16S rRNA\n- UNITE - eukaryotic nuclear ribosomal ITS region - ITS\n- Greengenes (only testing!)\n\nGenerally, using `silva`, `unite-fungi`, or `unite-alleuk` will select the most recent supported version. For testing purposes, the tiny database `greengenes85` (dereplicated at 85% sequence similarity) is available. For details on what values are valid, please either use an invalid value such as `x` (causing the pipeline to send an error message with all valid values) or see `conf/ref_databases.config`.",
                     "description": "Name of supported database, and optionally also version number",
-                    "enum": ["silva=138", "silva", "greengenes85", "greengenes2", "greengenes2=2022.10"]
+                    "enum": [
+                        "silva=138",
+                        "silva",
+                        "greengenes85",
+                        "greengenes2",
+                        "greengenes2=2022.10"
+                    ]
                 },
                 "qiime_ref_tax_custom": {
                     "type": "string",
@@ -529,7 +544,12 @@
                     "help_text": "If data is long read ITS sequences, that need to be cut to ITS region (full ITS, only ITS1, or only ITS2) for taxonomy assignment.",
                     "description": "Part of ITS region to use for taxonomy assignment: \"full\", \"its1\", or \"its2\"",
                     "default": "none",
-                    "enum": ["none", "full", "its1", "its2"]
+                    "enum": [
+                        "none",
+                        "full",
+                        "its1",
+                        "its2"
+                    ]
                 },
                 "its_partial": {
                     "type": "integer",
@@ -549,7 +569,13 @@
                     "type": "string",
                     "help_text": "",
                     "description": "Name of supported database, and optionally also version number",
-                    "enum": ["silva", "silva=128", "greengenes", "greengenes=13_8", "greengenes88"]
+                    "enum": [
+                        "silva",
+                        "silva=128",
+                        "greengenes",
+                        "greengenes=13_8",
+                        "greengenes88"
+                    ]
                 },
                 "sidle_ref_tax_custom": {
                     "type": "string",
@@ -681,7 +707,7 @@
                 },
                 "ancombc_effect_size": {
                     "type": "number",
-                    "default": 1,
+                    "default": 1.0,
                     "minimum": 0,
                     "description": "Effect size threshold for differential abundance barplot for `--ancombc` and `--ancombc_formula`",
                     "fa_icon": "fas fa-greater-than-equal"
@@ -822,7 +848,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {