Format changes in schema

Author: skrakau

nextflow_schema.json

@@ -390,12 +390,12 @@
                 "centrifuge_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with centrifuge.",
-                    "help_text": "E.g. \"ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz\"."
+                    "help_text": "E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
                 },
                 "kraken2_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with kraken2.",
-                    "help_text": "The database file must be a compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. \"ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz\"."
+                    "help_text": "The database file must be a compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
                 },
                 "skip_krona": {
                     "type": "boolean",
@@ -404,16 +404,16 @@
                 "cat_db": {
                     "type": "string",
                     "description": "Database for taxonomic classification of metagenome assembled genomes.",
-                    "help_text": "E.g. \"https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz\". This parameter is mutually exclusive with '--cat_db_generate'. The zipped file needs to contain a folder named '*taxonomy*' and '*database*' that hold the respective files."
+                    "help_text": "E.g. https://tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz. This parameter is mutually exclusive with `--cat_db_generate`. The zipped file needs to contain a folder named '*taxonomy*' and '*database*' that hold the respective files."
                 },
                 "cat_db_generate": {
                     "type": "boolean",
                     "description": "Generate CAT database.",
-                    "help_text": "Download the taxonomy files from NCBI taxonomy, the nr database and generate CAT database. This parameter is mutually exclusive with '--cat_db'. Useful to build a CAT database with the same DIAMOND version as used for running CAT classification, avoiding compatibility problems."
+                    "help_text": "Download the taxonomy files from NCBI taxonomy, the nr database and generate CAT database. This parameter is mutually exclusive with `--cat_db`. Useful to build a CAT database with the same DIAMOND version as used for running CAT classification, avoiding compatibility problems."
                 },
                 "save_cat_db": {
                     "type": "boolean",
-                    "description": "Save the CAT database generated when specified by '--cat_db_generate'.",
+                    "description": "Save the CAT database generated when specified by `--cat_db_generate`.",
                     "help_text": "Useful to allow reproducibility, as old versions of prebuild CAT databases do not always remain accessible and underlying NCBI taxonomy and nr databases change."
                 },
                 "gtdb": {