docs: Update schema and param docs

beiko-lab · Jul 25, 2024 · 0e23b10 · 0e23b10
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/docs/params.md b/docs/params.md
@@ -73,7 +73,7 @@ Parameters for the lineage subworkflow
 | `run_poppunk_qc` | Whether to run the QC step for PopPunk | `boolean` |  |
 | `enable_subsetting` | Enable subsetting workflow based on genome similarity | `boolean` |  |
 | `core_similarity` | Similarity threshold for core genomes | `number` | 99.9 |
-| `accessory_similarity` | Similarity threshold for accessory genes | `number` | 99 |
+| `accessory_similarity` | Similarity threshold for accessory genes | `number` | 99.0 |
 
 ## Gene Order
 
@@ -141,9 +141,9 @@ Set the top limit for requested resources for any single job.
 
 | Parameter | Description | Type | Default |
 |-----------|-----------|-----------|-----------|
-| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`</small></details>| `integer` | 16 |
-| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 128.GB |
-| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`</small></details>| `string` | 240.h |
+| `max_cpus` | Maximum number of CPUs that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`</small></details>| `integer` | 72 |
+| `max_memory` | Maximum amount of memory that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`</small></details>| `string` | 125.GB |
+| `max_time` | Maximum amount of time that can be requested for any single job. <details><summary>Help</summary><small>Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`</small></details>| `string` | 168.h |
 
 ## Generic options
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -226,7 +226,7 @@
                 },
                 "accessory_similarity": {
                     "type": "number",
-                    "default": 99,
+                    "default": 99.0,
                     "fa_icon": "far fa-clone",
                     "description": "Similarity threshold for accessory genes"
                 }
@@ -440,15 +440,15 @@
                 "max_cpus": {
                     "type": "integer",
                     "description": "Maximum number of CPUs that can be requested for any single job.",
-                    "default": 16,
+                    "default": 72,
                     "fa_icon": "fas fa-microchip",
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`"
                 },
                 "max_memory": {
                     "type": "string",
                     "description": "Maximum amount of memory that can be requested for any single job.",
-                    "default": "128.GB",
+                    "default": "125.GB",
                     "fa_icon": "fas fa-memory",
                     "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                     "hidden": true,
@@ -457,7 +457,7 @@
                 "max_time": {
                     "type": "string",
                     "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
+                    "default": "168.h",
                     "fa_icon": "far fa-clock",
                     "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$",
                     "hidden": true,