Bump shinyngs (#5543)

* Bump shinyngs * Fix containers * Migrate shinyngs/app to nf-test * Bump versions again * Bump conda envs too * Bump snapshots for versions * shinyngs/staticexploratory -> nftest * Appease eclint --------- Co-authored-by: Adam Talbot <[email protected]>
nf-core · May 2, 2024 · 2876a02 · 2876a02
1 parent 3f6c1f1
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Showing 23 changed files with 475 additions and 192 deletions.
diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.7
diff --git a/modules/nf-core/shinyngs/app/main.nf b/modules/nf-core/shinyngs/app/main.nf
@@ -15,8 +15,8 @@ process SHINYNGS_APP {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.7--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.7--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)    // Experiment-level info
@@ -49,8 +49,23 @@ process SHINYNGS_APP {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
         r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+
+    """
+    mkdir -p $prefix
+    touch ${prefix}/data.rds
+    touch ${prefix}/app.R
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
+    END_VERSIONS
+    """
+
 }
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test b/modules/nf-core/shinyngs/app/tests/main.nf.test
@@ -0,0 +1,133 @@
+nextflow_process {
+
+    name "Test Process SHINYNGS_APP"
+    script "../main.nf"
+    process "SHINYNGS_APP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "shinyngs"
+    tag "shinyngs/app"
+
+    test("mouse - multi matrix") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                raw_expression_matrix_file.copyTo('normalised.tsv')
+                normalised_expression_matrix_file = file('normalised.tsv') 
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file, normalised_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("mouse - single matrix") {
+
+        config './nextflow.config'
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("mouse - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                expression_test_data_dir = params.modules_testdata_base_path + 'genomics/mus_musculus/rnaseq_expression/'
+
+                expression_sample_sheet = file(expression_test_data_dir + 'SRP254919.samplesheet.csv', checkIfExists: true)
+                expression_feature_meta = file(expression_test_data_dir + 'SRP254919.gene_meta.tsv', checkIfExists: true)
+                raw_expression_matrix_file = file(expression_test_data_dir + 'SRP254919.salmon.merged.gene_counts.top1000cov.tsv', checkIfExists: true)
+                expression_contrasts = file(expression_test_data_dir + 'SRP254919.contrasts.csv', checkIfExists: true)
+                expression_differential = file(expression_test_data_dir + 'SRP254919.salmon.merged.deseq2.results.tsv', checkIfExists: true)
+
+                // Copy some inputs for testing the multi-matrix functionality
+                expression_differential.copyTo('second_contrast_stats.tsv')
+                second_contrast_stats = file('second_contrast_stats.tsv')
+
+                contrast_stats_assay = Channel.value(1)
+
+                input[0] = [ [ "id":"SRP254919" ], expression_sample_sheet,  expression_feature_meta, [ raw_expression_matrix_file ] ]
+                input[1] = [ [ "id":"SRP254919" ], expression_contrasts, [ expression_differential, second_contrast_stats  ] ]
+                input[2] = contrast_stats_assay 
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.app[0][1]).name,
+                    process.out.app[0][2],
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-core/shinyngs/app/tests/main.nf.test.snap b/modules/nf-core/shinyngs/app/tests/main.nf.test.snap
@@ -0,0 +1,44 @@
+{
+    "mouse - stub": {
+        "content": [
+            "data.rds",
+            "app.R:md5,d41d8cd98f00b204e9800998ecf8427e",
+            [
+                "versions.yml:md5,09111b64e01c10c1c0788e9700488e5c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T15:29:41.473618"
+    },
+    "mouse - multi matrix": {
+        "content": [
+            "data.rds",
+            "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
+            [
+                "versions.yml:md5,09111b64e01c10c1c0788e9700488e5c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T15:29:06.587538"
+    },
+    "mouse - single matrix": {
+        "content": [
+            "data.rds",
+            "app.R:md5,bedcfc45b6cdcc2b8fe3627987e2b17a",
+            [
+                "versions.yml:md5,09111b64e01c10c1c0788e9700488e5c"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-02T15:29:26.649048"
+    }
+}
diff --git a/...ules/nf-core/shinyngs/app/nextflow.config → ...f-core/shinyngs/app/tests/nextflow.config b/...ules/nf-core/shinyngs/app/nextflow.config → ...f-core/shinyngs/app/tests/nextflow.config
@@ -1,12 +1,8 @@
 process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
     //withName: test_shinyngs_app:SHINYNGS_APP {
     //    secret 'SHINYAPPS_TOKEN'                                                  
     //    secret 'SHINYAPPS_SECRET'  
     //}
-
     withName: test_shinyngs_app:SHINYNGS_APP {
         ext.prefix = { "${meta.id}_test" }
         ext.args = { "--contrast_stats_assay 1" }

diff --git a/modules/nf-core/shinyngs/app/tests/tags.yml b/modules/nf-core/shinyngs/app/tests/tags.yml
@@ -0,0 +1,2 @@
+shinyngs/app:
+  - "modules/nf-core/shinyngs/app/**"
diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.7
diff --git a/modules/nf-core/shinyngs/staticdifferential/main.nf b/modules/nf-core/shinyngs/staticdifferential/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICDIFFERENTIAL {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.7--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.7--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(differential_result)                              // Differential info: contrast and differential stats

diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::r-shinyngs=1.8.5
+  - bioconda::r-shinyngs=1.8.7
diff --git a/modules/nf-core/shinyngs/staticexploratory/main.nf b/modules/nf-core/shinyngs/staticexploratory/main.nf
@@ -4,8 +4,8 @@ process SHINYNGS_STATICEXPLORATORY {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.5--r43hdfd78af_0' :
-        'biocontainers/r-shinyngs:1.8.5--r43hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/r-shinyngs:1.8.7--r43hdfd78af_0' :
+        'biocontainers/r-shinyngs:1.8.7--r43hdfd78af_0' }"
 
     input:
     tuple val(meta), path(sample), path(feature_meta), path(assay_files)
@@ -43,7 +43,29 @@ process SHINYNGS_STATICEXPLORATORY {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: meta.id
+    """
+    mkdir -p ${prefix}/png ${prefix}/html
+    touch ${prefix}/png/boxplot.png
+    touch ${prefix}/html/boxplot.html
+    touch ${prefix}/png/density.png
+    touch ${prefix}/html/density.html
+    touch ${prefix}/png/pca2d.png
+    touch ${prefix}/html/pca3d.html
+    touch ${prefix}/png/pca3d.png
+    touch ${prefix}/html/pca2d.html
+    touch ${prefix}/png/mad_correlation.png
+    touch ${prefix}/html/mad_correlation.html
+    touch ${prefix}/png/sample_dendrogram.png
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
         r-shinyngs: \$(Rscript -e "library(shinyngs); cat(as.character(packageVersion('shinyngs')))")
     END_VERSIONS
     """