fixed

bigbio · Feb 26, 2024 · d2ccd5f · d2ccd5f
1 parent ea2fdf2
commit d2ccd5f
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Showing 2 changed files with 4 additions and 16 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -295,7 +295,6 @@
                 "instrument": {
                     "type": "string",
                     "description": "Type of instrument that generated the data. 'low_res' or 'high_res' (default; refers to LCQ and LTQ instruments)",
-                    "default": null,
                     "fa_icon": "fas fa-list-ol"
                 },
                 "protocol": {
@@ -461,7 +460,7 @@
                 "run_fdr_cutoff": {
                     "type": "number",
                     "description": "FDR cutoff on PSM level (or peptide level; see Percolator options) *per run* before going into feature finding, map alignment and inference. This can be seen as a pre-filter. See ",
-                    "default": 0.10,
+                    "default": 0.1,
                     "fa_icon": "fas fa-filter"
                 },
                 "idfilter_debug": {
@@ -905,7 +904,7 @@
                 "feature_with_id_min_score": {
                     "type": "number",
                     "description": "The minimum probability (e.g.: 0.25) an identified (=id targeted) feature must have to be kept for alignment and linking (0=no filter).",
-                    "default": 0.10,
+                    "default": 0.1,
                     "fa_icon": "fas fa-filter",
                     "help_text": "The minimum probability (e.g.: 0.25) an identified (=id targeted) feature must have to be kept for alignment and linking (0=no filter). (default: '0.0') (min: '0.0' max: '1.0')"
                 },
@@ -1277,6 +1276,7 @@
                 "max_memory": {
                     "type": "string",
                     "description": "Maximum amount of memory that can be requested for any single job.",
+                    "default": "128 GB",
                     "fa_icon": "fas fa-memory",
                     "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
                     "hidden": true,
@@ -1285,6 +1285,7 @@
                 "max_time": {
                     "type": "string",
                     "description": "Maximum amount of time that can be requested for any single job.",
+                    "default": "10d",
                     "fa_icon": "far fa-clock",
                     "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                     "hidden": true,

diff --git a/workflows/quantms.nf b/workflows/quantms.nf
@@ -23,19 +23,6 @@ include { FILE_PREPARATION } from '../subworkflows/local/file_preparation'
 include { CREATE_INPUT_CHANNEL } from '../subworkflows/local/create_input_channel'
 include { DDA_ID } from '../subworkflows/local/dda_id'
 
-/*
-========================================================================================
-    IMPORT NF-CORE MODULES/SUBWORKFLOWS
-========================================================================================
-*/
-
-//
-// MODULE: Installed directly from nf-core/modules
-//
-
-include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
-
-
 
 /*
 ========================================================================================