Merge pull request #284 from nf-core/dev

Update dev-ratio with changes from dev branch

CHANGELOG.md

@@ -9,7 +9,10 @@ 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))
+- [[#282](https://github.com/nf-core/differentialabundance/pull/282)] - In order to improve resumability, create a copy of the matrix as an annotation file only if necessary; add original matrix file name to copy name ([@bjlang](https://github.com/bjlang), review by [@WackerO](https://github.com/WackerO))
 
 ### Changed
 
@@ -32,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [[#278](https://github.com/nf-core/differentialabundance/pull/278)] - Fix missing ch_gene_sets when running gprofiler without gene sets ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#267](https://github.com/nf-core/differentialabundance/pull/267)] - Whitespace fix, remove TODO, also update changelog for release release 1.5.0 ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#265](https://github.com/nf-core/differentialabundance/pull/265)] - GSEA- pngs and htmls in same place ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#257](https://github.com/nf-core/differentialabundance/pull/257)] - Fixed FILTER_DIFFTABLE module, updated PROTEUS module to better handle whitespace in prefix param, made docs clearer ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

assets/differentialabundance_report.Rmd

@@ -487,7 +487,7 @@ display_columns <- head(union(display_columns, additional_useful_cols), 5)
 display_columns <- unique(c(display_columns, informative_variables))
 observations_to_print <- observations[,unique(display_columns)]
 colnames(observations_to_print) <- prettifyVariablename(colnames(observations_to_print))
-print( htmltools::tagList(datatable(observations_to_print, caption = paste(ucfirst(params$observations_type), 'metadata'), rownames = FALSE, options = list(dom = 'tb')) ))
+print( htmltools::tagList(datatable(observations_to_print, caption = paste(ucfirst(params$observations_type), 'metadata'), rownames = FALSE, options = list(dom = 'tp')) ))
 ```
 
 ## Contrasts

assets/multiqc_config.yml

@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/releases/tag/1.5.0" target="_blank">nf-core/differentialabundance</a>
+  This report has been generated by the <a href="https://github.com/nf-core/differentialabundance/tree/dev" target="_blank">nf-core/differentialabundance</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/differentialabundance/1.5.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/differentialabundance/dev/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-differentialabundance-methods-description":

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

@@ -92,22 +92,22 @@
                     },
                     "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
@@ -416,7 +415,7 @@ manifest {
     description     = 'Differential abundance analysis'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.10.0'
-    version         = '1.5.0'
+    version         = '1.6.0dev'
     doi             = '10.5281/zenodo.7568000'
 }
 

nextflow_schema.json

@@ -989,12 +989,6 @@
                     "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

@@ -62,6 +62,7 @@ if (params.control_features) { ch_control_features = Channel.of([ exp_meta, file
 def run_gene_set_analysis = params.gsea_run || params.gprofiler2_run
 
 if (run_gene_set_analysis) {
+    ch_gene_sets = Channel.of([])    // For methods that can run without gene sets
     if (params.gene_sets_files) {
         gene_sets_files = params.gene_sets_files.split(",")
         ch_gene_sets = Channel.of(gene_sets_files).map { file(it, checkIfExists: true) }
@@ -74,8 +75,6 @@ if (run_gene_set_analysis) {
         if (!params.gprofiler2_token && !params.gprofiler2_organism) {
             error("To run gprofiler2, please provide a run token, GMT file or organism!")
         }
-    } else {
-        ch_gene_sets = []    // For methods that can run without gene sets
     }
 }
 
@@ -254,15 +253,16 @@ workflow DIFFERENTIALABUNDANCE {
 
         // Otherwise we can just use the matrix input; save it to the workdir so that it does not
         // just appear wherever the user runs the pipeline
-        matrix_as_anno_filename = "${workflow.workDir}/matrix_as_anno.${matrix_file.getExtension()}"
+        matrix_as_anno_filename = "${workflow.workDir}/${matrix_file.getBaseName()}_as_anno.${matrix_file.getExtension()}"
         if (params.study_type == 'maxquant'){
             ch_features_matrix = ch_in_norm
         } else {
             ch_features_matrix = ch_in_raw
         }
         ch_features = ch_features_matrix
             .map{ meta, matrix ->
-                matrix.copyTo(matrix_as_anno_filename)
+                matrix_copy = file(matrix_as_anno_filename)
+                matrix_copy.exists() && matrix.getText().md5().equals(matrix_copy.getText().md5()) ?: matrix.copyTo(matrix_as_anno_filename)
                 [ meta, file(matrix_as_anno_filename) ]
             }
     }
@@ -585,9 +585,9 @@ 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{