Merge pull request #266 from nf-core/fix_logging

Fix logging by specifying assays to log

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- [[#266](https://github.com/nf-core/differentialabundance/pull/266)] - Fix logging by specifying assays to log ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#259](https://github.com/nf-core/differentialabundance/pull/259)] - Bump gtf2featureannotation to fix GTF handling error ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
 - [[#257](https://github.com/nf-core/differentialabundance/pull/257)] - Added maxquant profile to nextflow.config to make it available ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
 - [[#254](https://github.com/nf-core/differentialabundance/pull/254)] - Some parameter changes, added qbic credits ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

assets/differentialabundance_report.Rmd

@@ -38,7 +38,7 @@ params:
     features_metadata_cols: NULL
     features_gtf_feature_type: NULL
     features_gtf_table_first_field: NULL
-    features_log2_assays: NULL
+    exploratory_log2_assays: NULL
     raw_matrix: null                                            # e.g. 0_salmon.merged.gene_counts_length_scaled.tsv
     normalised_matrix: null
     variance_stabilised_matrix: null                            # e.g. test_files/3_treatment-WT-P23H.vst.tsv
@@ -310,11 +310,12 @@ assay_data <- lapply(assay_files, function(x) {
     mat
 })
 
-if (!is.null(params$features_log2_assays)) {
+log2_assays <- params$exploratory_log2_assays
+if (!is.null(log2_assays)) {
     # Remove brackets from assay list. TODO: remove if this is added to cond_log2_transform_assays
-    params$features_log2_assays <- gsub('\\]$', '', gsub('^\\[', '', params$features_log2_assays))
+    log2_assays <- gsub('\\]$', '', gsub('^\\[', '', log2_assays))
 }
-assay_data <- cond_log2_transform_assays(assay_data, params$features_log2_assays)
+assay_data <- cond_log2_transform_assays(assay_data, log2_assays, prettify_names = FALSE)
 
 # Now we can rename the observations rows using the title field
 rownames(observations) <- observations[[observations_name_col]]

conf/affy.config

@@ -27,6 +27,7 @@ params {
     // Exploratory
     exploratory_assay_names = 'raw,normalised'
     exploratory_final_assay = 'normalised'
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"

conf/maxquant.config

@@ -28,6 +28,7 @@ params {
     // Exploratory
     exploratory_assay_names = "raw,normalised"
     exploratory_final_assay = "normalised"
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"

conf/modules.config

@@ -375,7 +375,7 @@ process {
             "--final_assay \"${params.exploratory_final_assay}\"",
             "--outlier_mad_threshold ${params.exploratory_mad_threshold}",
             "--palette_name \"${params.exploratory_palette_name}\"",
-            ( (params.study_type == 'maxquant') ? "--log2_assays ''" : (((params.features_log2_assays == null) ? '' : "--log2_assays \"$params.features_log2_assays\"".replace('[', '').replace(']', ''))) )
+            ( (params.study_type == 'maxquant') ? "--log2_assays ''" : (((params.exploratory_log2_assays == null) ? '' : "--log2_assays \"$params.exploratory_log2_assays\"".replace('[', '').replace(']', ''))) )
         ].join(' ').trim() }
     }
 
@@ -428,8 +428,8 @@ process {
     }
 
     withName: RMARKDOWNNOTEBOOK {
-        conda = "bioconda::r-shinyngs=1.8.4"
-        container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.4--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.4--r43hdfd78af_0' }" }
+        conda = "bioconda::r-shinyngs=1.8.8"
+        container = { "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.8--r43hdfd78af_0' : 'biocontainers/r-shinyngs:1.8.8--r43hdfd78af_0' }" }
         publishDir = [
             [
                 path: { "${params.outdir}/report" },

conf/rnaseq.config

@@ -27,6 +27,7 @@ params {
     // Exploratory
     exploratory_assay_names = "raw,normalised,variance_stabilised"
     exploratory_final_assay = "variance_stabilised"
+    exploratory_log2_assays = 'raw,normalised'
 
     // Differential options
     differential_file_suffix         = ".deseq2.results.tsv"

conf/soft.config

@@ -33,6 +33,7 @@ params {
     // Exploratory
     exploratory_assay_names = 'normalised'
     exploratory_final_assay = 'normalised'
+    exploratory_log2_assays = null
 
     // Differential options
     differential_file_suffix         = ".limma.results.tsv"

modules.json

@@ -72,22 +72,22 @@
                     },
                     "shinyngs/app": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticdifferential": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/staticexploratory": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "shinyngs/validatefomcomponents": {
                         "branch": "master",
-                        "git_sha": "d2d6072ae4c3a9d394dfe773bb0751f34df7a896",
+                        "git_sha": "85519fe9deccf2c5f7ff1f3b5d3494c61a794643",
                         "installed_by": ["modules"]
                     },
                     "untar": {
@@ -111,7 +111,7 @@
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfvalidation_plugin": {