Add exists to Schema

CHANGELOG.md

@@ -9,6 +9,7 @@
   - Removes problematic `-m` memory assignment for samtools sort [#81](https://github.com/nf-core/methylseq/issues/81)
 - Use `fromSamplesheet` from nf-validation [#341](https://github.com/nf-core/methylseq/pull/341)
 - Update Maintainers and add CODEOWNERS [#345](https://github.com/nf-core/methylseq/pull/345)
+- Update schema to utilize exists and add more patterns [#342](https://github.com/nf-core/methylseq/pull/342)
 
 ### Bug fixes & refactoring
 

nextflow_schema.json

@@ -98,26 +98,29 @@
                     "format": "file-path",
                     "exists": true,
                     "mimetype": "text/plain",
-                    "pattern": "^\\S+\\.fn?a(sta)?$",
+                    "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$",
                     "description": "Path to FASTA genome file",
                     "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible. You can use the command line option `--save_reference` to keep the generated references so that they can be added to your config and used again in the future. If aligner is Bismark and bismark_index is specified, this parameter is ignored."
                 },
                 "fasta_index": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.fn?a(sta)?.fai$",
                     "description": "Path to Fasta index file.",
                     "help_text": "The FASTA index file (`.fa.fai`) is only needed when using the bwa_meth aligner. It is used by MethylDackel. If using Bismark this parameter is ignored.",
                     "fa_icon": "fas fa-bookmark"
                 },
                 "bismark_index": {
                     "type": "string",
-                    "format": "directory-path",
+                    "format": "path",
                     "description": "Path to a directory containing a Bismark reference index.",
                     "fa_icon": "fas fa-dot-circle"
                 },
                 "bwa_meth_index": {
                     "type": "string",
-                    "format": "directory-path",
+                    "format": "path",
                     "description": "bwameth index filename base",
                     "help_text": "Directory for a bwa-meth genome reference index. Only used when using the bwa-meth aligner.\n\nNote that this is not a complete path, but the directory containing the reference. For example, if you have file paths such as `/path/to/ref/genome.fa.bwameth.c2t.bwt`, you should specify `/path/to/ref/`.",
                     "fa_icon": "far fa-dot-circle"
@@ -339,6 +342,9 @@
                 },
                 "known_splices": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "pattern": "^\\S+\\.gtf(\\.gz)?$",
                     "description": "Supply a .gtf file containing known splice sites (bismark_hisat only).",
                     "help_text": "Specify to run Bismark with the `--known-splicesite-infile` flag to run splice-aware alignment using HISAT2. A `.gtf` file has to be provided from which a list of known splicesites is created by the pipeline\n\n> NB: This only works when using the `bismark_hisat` aligner with `--align`",
                     "fa_icon": "fas fa-barcode"
@@ -403,7 +409,10 @@
             "default": "",
             "properties": {
                 "bamqc_regions_file": {
-                    "type": "string",
+                    "format": "file-path",
+                    "exists": true,
+                    "mimetype": "text/plain",
+                    "pattern": "^\\S+\\.gff|\\.bed(\\.gz)?$",
                     "description": "A GFF or BED file containing the target regions which will be passed to Qualimap/Bamqc.",
                     "help_text": "Setting this option could be useful if you want calculate coverage stats over a list of regions, i.e. for targeted methylation sequencing data."
                 }