fixed

bigbio · Feb 26, 2024 · ea2fdf2 · ea2fdf2
1 parent 1ed3ce2
commit ea2fdf2
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Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -295,7 +295,7 @@
                 "instrument": {
                     "type": "string",
                     "description": "Type of instrument that generated the data. 'low_res' or 'high_res' (default; refers to LCQ and LTQ instruments)",
-                    "default": "high_res",
+                    "default": null,
                     "fa_icon": "fas fa-list-ol"
                 },
                 "protocol": {
@@ -461,7 +461,7 @@
                 "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": 0.01,
+                    "default": 0.10,
                     "fa_icon": "fas fa-filter"
                 },
                 "idfilter_debug": {
@@ -905,7 +905,7 @@
                 "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": 0.0,
+                    "default": 0.10,
                     "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')"
                 },
@@ -1277,7 +1277,6 @@
                 "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$",
                     "hidden": true,
@@ -1286,7 +1285,6 @@
                 "max_time": {
                     "type": "string",
                     "description": "Maximum amount of time that can be requested for any single job.",
-                    "default": "240.h",
                     "fa_icon": "far fa-clock",
                     "pattern": "^(\\d+\\.?\\s*(s|m|h|d|day)\\s*)+$",
                     "hidden": true,
@@ -1484,4 +1482,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}
diff --git a/workflows/quantms.nf b/workflows/quantms.nf
@@ -135,14 +135,16 @@ workflow QUANTMS {
         ch_msstats_in = ch_msstats_in.mix(LFQ.out.msstats_in)
         ch_versions = ch_versions.mix(LFQ.out.versions.ifEmpty(null))
 
-    DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign, FILE_PREPARATION.out.statistics)
-    ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report)
-    ch_msstats_in = ch_msstats_in.mix(DIA.out.msstats_in)
+        DIA(ch_fileprep_result.dia, CREATE_INPUT_CHANNEL.out.ch_expdesign, FILE_PREPARATION.out.statistics)
+        ch_pipeline_results = ch_pipeline_results.mix(DIA.out.diann_report)
+        ch_msstats_in = ch_msstats_in.mix(DIA.out.msstats_in)
+        ch_versions = ch_versions.mix(DIA.out.versions.ifEmpty(null))
+    }
 
     //
     // Collate and save software versions
     //
-    DIA.out.versions.mix(LFQ.out.versions).mix(TMT.out.versions).mix(ch_versions)
+    ch_versions
             .branch {
                 yaml : it.asBoolean()
                 other : true