Bump shinyngs, fix contrasts passed to app creation

CHANGELOG.md

@@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
+- [[#280](https://github.com/nf-core/differentialabundance/pull/280)] - Bump shinyngs, fix contrasts passed to app creation ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#274](https://github.com/nf-core/differentialabundance/pull/274)] - Fix pagination on samples table ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#272](https://github.com/nf-core/differentialabundance/pull/272)] - Show >10 contrasts in report ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 

conf/modules.config

@@ -420,7 +420,7 @@ process {
             ((params.report_title == null) ? '' : "--title \"$params.report_title\""),
             ((params.report_author == null) ? '' : "--author \"$params.report_author\""),
             ((params.report_description == null) ? '' : "--description \"$params.report_description\""),
-            ((params.shinyngs_guess_unlog_matrices) ? "--guess_unlog_matrices" : ''),
+            ( (params.study_type == 'maxquant') ? "--log2_assays ''" : (((params.exploratory_log2_assays == null) ? '' : "--log2_assays \"$params.exploratory_log2_assays\"".replace('[', '').replace(']', ''))) ),
             ((params.shinyngs_deploy_to_shinyapps_io) ? "--deploy_app" : ''),
             ((params.shinyngs_shinyapps_account == null) ? '' : "--shinyapps_account \"$params.shinyngs_shinyapps_account\""),
             ((params.shinyngs_shinyapps_app_name == null) ? '' : "--shinyapps_name \"$params.shinyngs_shinyapps_app_name\"")

modules.json

@@ -72,22 +72,22 @@
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
+                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
+                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
+                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
+                        "git_sha": "91fc36585a50f9bae98cb5b3dff36ce64c83a6b4",
                         "installed_by": ["modules"]
                     },
                     "untar": {

nextflow.config

@@ -176,7 +176,6 @@ params {
 
     // ShinyNGS
     shinyngs_build_app              = true
-    shinyngs_guess_unlog_matrices   = true
 
     // Note: for shinyapps deployment, in addition to setting these values,
     // SHINYAPPS_TOKEN and SHINYAPPS_SECRET must be available to the

nextflow_schema.json

@@ -979,12 +979,6 @@
                     "default": "null",
                     "description": "The name of the app to push to in your shinyapps.io account",
                     "fa_icon": "fas fa-file-signature"
-                },
-                "shinyngs_guess_unlog_matrices": {
-                    "type": "boolean",
-                    "default": true,
-                    "description": "Should we guess the log status of matrices and unlog for the app?",
-                    "help_text": "In the app context, it's usually helpful if things are not in log scale, so that e.g. fold changes make some sense with respect to observed values. This flag will cause the shinyngs app-building script to make a guess based on observed values as to the log status of input matrices, and adjust the loading accordingly."
                 }
             },
             "fa_icon": "fab fa-app-store-ios"

workflows/differentialabundance.nf

@@ -584,9 +584,9 @@ workflow DIFFERENTIALABUNDANCE {
         // Make a new contrasts file from the differential metas to guarantee the
         // same order as the differential results
 
-        ch_app_differential = ch_differential.first().map{it[0].keySet().join(',')}
+        ch_app_differential = ch_differential.first().map{it[0].keySet().tail().join(',')}
             .concat(
-                ch_differential.map{it[0].values().join(',')}
+                ch_differential.map{it[0].values().tail().join(',')}
             )
             .collectFile(name: 'contrasts.csv', newLine: true, sort: false)
             .map{