From ea2fdf26c10e2d3f0f60d25a0dcb2612480666b9 Mon Sep 17 00:00:00 2001
From: Chengxin Dai <37200167+daichengxin@users.noreply.github.com>
Date: Mon, 26 Feb 2024 10:47:22 +0800
Subject: [PATCH] fixed

---
 nextflow_schema.json | 10 ++++------
 workflows/quantms.nf | 10 ++++++----
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 60496d69..684175e3 100644
--- 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"
         }
     ]
-}
\ No newline at end of file
+}
diff --git a/workflows/quantms.nf b/workflows/quantms.nf
index cbe06b73..27418746 100644
--- 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