Update shinyngs, remove na.omit() from proteus (nf-core#3707)

* Added log_assays param to shinyngs tests, updated shinyngs containers, removed na.omit() from proteus * Updated shinyngs containers, added test for plot_exploratory --log_assays param * added --log2_assays flag back into nextflow.config * removed redundant process definition * prettier, updated proteus tests
asp8200 · Aug 8, 2023 · 707c31e · 707c31e
1 parent 8c4542e
commit 707c31e
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Showing 11 changed files with 52 additions and 23 deletions.
diff --git a/modules/nf-core/proteus/readproteingroups/templates/proteus_readproteingroups.R b/modules/nf-core/proteus/readproteingroups/templates/proteus_readproteingroups.R
@@ -266,7 +266,7 @@ for (normfun in unlist(strsplit(opt\$normfuns, ","))) {
 
     # Apply log2 and remove NAs as these will otherwise mess with some of the following modules
 
-    proteinGroups.normalized\$tab <- na.omit(log2(proteinGroups.normalized\$tab))
+    proteinGroups.normalized\$tab <- log2(proteinGroups.normalized\$tab)
 
     png(paste(output_prefix, 'proteus', normfun, 'normalized_distributions.png', sep='.'), width = 5*300, height = 5*300, res = 300, pointsize = 8)
     print(
@@ -317,7 +317,7 @@ for (normfun in unlist(strsplit(opt\$normfuns, ","))) {
 
 # Process and save raw table
 
-proteinGroups\$tab <- na.omit(log2(proteinGroups\$tab))
+proteinGroups\$tab <- log2(proteinGroups\$tab)
 
 # Generate raw distribution plot
 

diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
@@ -13,10 +13,10 @@ process SHINYNGS_APP {
     //
     // Those values must then be set in your Nextflow secrets.
 
-    conda "bioconda::r-shinyngs=1.7.2"
+    conda "bioconda::r-shinyngs=1.8.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.2--r42hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.7.2--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.1--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.1--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)    // Experiment-level info

diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
@@ -2,10 +2,10 @@ process SHINYNGS_STATICDIFFERENTIAL {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::r-shinyngs=1.7.2"
+    conda "bioconda::r-shinyngs=1.8.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.2--r42hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.7.2--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.1--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.1--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(differential_result)                              // Differential info: contrast and differential stats

diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -2,10 +2,10 @@ process SHINYNGS_STATICEXPLORATORY {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::r-shinyngs=1.7.2"
+    conda "bioconda::r-shinyngs=1.8.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.2--r42hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.7.2--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.1--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.1--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)

diff --git a/modules/nf-core/shinyngs/validatefomcomponents/main.nf b/modules/nf-core/shinyngs/validatefomcomponents/main.nf
@@ -2,10 +2,10 @@ process SHINYNGS_VALIDATEFOMCOMPONENTS {
     tag "$sample"
     label 'process_single'
 
-    conda "bioconda::r-shinyngs=1.7.2"
+    conda "bioconda::r-shinyngs=1.8.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.7.2--r42hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.7.2--r42hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.1--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.1--r43hdfd78af_0' }"
 
     input:
     tuple val(meta),  path(sample), path(assay_files)

diff --git a/tests/modules/nf-core/proteus/readproteingroups/test.yml b/tests/modules/nf-core/proteus/readproteingroups/test.yml
@@ -9,17 +9,17 @@
     - path: output/proteus/Celltype.proteus.normalizeMedian.normalized_mean_variance_relationship.png
     - path: output/proteus/Celltype.proteus.normalizeMedian.normalized_proteingroups.rds
     - path: output/proteus/Celltype.proteus.normalizeMedian.normalized_proteingroups_tab.tsv
-      md5sum: 07290a3ccd10019fb4e147f805b3e279
+      md5sum: 408db435ce25eef98b82b17c9515c7cb
     - path: output/proteus/Celltype.proteus.normalizeQuantiles.normalized_dendrogram.png
     - path: output/proteus/Celltype.proteus.normalizeQuantiles.normalized_distributions.png
     - path: output/proteus/Celltype.proteus.normalizeQuantiles.normalized_mean_variance_relationship.png
     - path: output/proteus/Celltype.proteus.normalizeQuantiles.normalized_proteingroups.rds
     - path: output/proteus/Celltype.proteus.normalizeQuantiles.normalized_proteingroups_tab.tsv
-      md5sum: 590dd593bb00617254964da4adfcffd9
+      md5sum: 4a0a74febfc6ba921210f465e890ff5b
     - path: output/proteus/Celltype.proteus.raw_distributions.png
     - path: output/proteus/Celltype.proteus.raw_proteingroups.rds
     - path: output/proteus/Celltype.proteus.raw_proteingroups_tab.tsv
-      md5sum: a0943baaa48ea76bdb8c80a580dc9953
+      md5sum: af7a556997b82f4ba38bfae8a6b91301
     - path: output/proteus/R_sessionInfo.log
       contains: ["proteus_0.2.16", "plotly_4.10.2", "ggplot2_3.4.2", "limma_3.54.0 "]
     - path: output/proteus/versions.yml
diff --git a/tests/modules/nf-core/shinyngs/app/test.yml b/tests/modules/nf-core/shinyngs/app/test.yml
@@ -7,7 +7,7 @@
     - path: output/shinyngs/SRP254919/app.R
       md5sum: bedcfc45b6cdcc2b8fe3627987e2b17a
     - path: output/shinyngs/SRP254919/data.rds
-      md5sum: e44dcb923603fae634687219e086b4af
+      md5sum: d6772b22b6e4708ae610fb9ad0b09db0
     - path: output/shinyngs/versions.yml
 
 - name: shinyngs app test_shinyngs_app_single_matrix
@@ -19,5 +19,5 @@
     - path: output/shinyngs/SRP254919/app.R
       md5sum: bedcfc45b6cdcc2b8fe3627987e2b17a
     - path: output/shinyngs/SRP254919/data.rds
-      md5sum: 40935136af5264cebd85e6d63c95b5f9
+      md5sum: 2a8c07908642e5273d03e922f4ac56fc
     - path: output/shinyngs/versions.yml
diff --git a/tests/modules/nf-core/shinyngs/staticdifferential/test.yml b/tests/modules/nf-core/shinyngs/staticdifferential/test.yml
@@ -13,5 +13,6 @@
     - shinyngs
   files:
     - path: output/shinyngs/hND6_vs_mCherry_test/html/volcano.html
-      contains: ["-4.0303380084,-0.0628302706,-0.3602268157,-0.6082456431", "higher in mCherry"]
+      contains:
+        ["-4.0303380084000002,-0.062830270600000002,-0.36022681569999998,-0.60824564309999996", "higher in mCherry"]
     - path: output/shinyngs/hND6_vs_mCherry_test/png/volcano.png
diff --git a/tests/modules/nf-core/shinyngs/staticexploratory/main.nf b/tests/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -15,6 +15,17 @@ workflow test_shinyngs_staticexploratory {
     )
 }
 
+workflow test_shinyngs_staticexploratory_specify_log {
+
+    expression_sample_sheet = file(params.test_data['mus_musculus']['genome']['rnaseq_samplesheet'], checkIfExists: true) 
+    expression_feature_meta = file(params.test_data['mus_musculus']['genome']['rnaseq_genemeta'], checkIfExists: true) 
+    expression_matrix_file = file(params.test_data['mus_musculus']['genome']['rnaseq_matrix'], checkIfExists: true) 
+
+    SHINYNGS_STATICEXPLORATORY ( 
+        [ [ "id":"treatment" ], expression_sample_sheet, expression_feature_meta, [ expression_matrix_file ] ],
+    )
+}
+
 workflow test_shinyngs_staticexploratory_html {
 
     expression_sample_sheet = file(params.test_data['mus_musculus']['genome']['rnaseq_samplesheet'], checkIfExists: true) 

diff --git a/tests/modules/nf-core/shinyngs/staticexploratory/nextflow.config b/tests/modules/nf-core/shinyngs/staticexploratory/nextflow.config
@@ -1,8 +1,12 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+    withName: 'test_shinyngs_staticexploratory_specify_log:SHINYNGS_STATICEXPLORATORY' {
+        ext.args = { "--log2_assays '1'" }
+    }
 
     withName: 'test_shinyngs_staticexploratory_html:SHINYNGS_STATICEXPLORATORY' {
         ext.args = { "--write_html" }
     }
-}
+}
diff --git a/tests/modules/nf-core/shinyngs/staticexploratory/test.yml b/tests/modules/nf-core/shinyngs/staticexploratory/test.yml
@@ -11,6 +11,19 @@
     - path: output/shinyngs/treatment/png/pca3d.png
     - path: output/shinyngs/treatment/png/sample_dendrogram.png
 
+- name: shinyngs staticexploratory test_shinyngs_staticexploratory_specify_log
+  command: nextflow run ./tests/modules/nf-core/shinyngs/staticexploratory -entry test_shinyngs_staticexploratory_specify_log -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shinyngs/staticexploratory/nextflow.config
+  tags:
+    - shinyngs/staticexploratory
+    - shinyngs
+  files:
+    - path: output/shinyngs/treatment/png/boxplot.png
+    - path: output/shinyngs/treatment/png/density.png
+    - path: output/shinyngs/treatment/png/mad_correlation.png
+    - path: output/shinyngs/treatment/png/pca2d.png
+    - path: output/shinyngs/treatment/png/pca3d.png
+    - path: output/shinyngs/treatment/png/sample_dendrogram.png
+
 - name: shinyngs staticexploratory test_shinyngs_staticexploratory_html
   command: nextflow run ./tests/modules/nf-core/shinyngs/staticexploratory -entry test_shinyngs_staticexploratory_html -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/shinyngs/staticexploratory/nextflow.config
   tags:
@@ -20,9 +33,9 @@
     - path: output/shinyngs/treatment/html/boxplot.html
       contains: ["SRX8042381", ' ENSMUSG00000027456","Gm37080']
     - path: output/shinyngs/treatment/html/density.html
-      contains: ["4.34767786283394,4.38328343135943,4.41888899988492"]
+      contains: ["4.3476778628339403,4.3832834313594287,4.4188889998849188"]
     - path: output/shinyngs/treatment/html/mad_correlation.html
-      contains: ["0,-0.742952800676994,0.674490759476595,-0.674490759476595"]
+      contains: ["0,-0.74295280067699376,0.67449075947659531,-0.6744907594765952"]
     - path: output/shinyngs/treatment/html/pca2d.html
       contains: ['SRX8042381","SRX8042382']
     - path: output/shinyngs/treatment/html/pca3d.html