Create gene heatmap nftest

CHANGELOG.md

@@ -7,9 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#94](https://github.com/nf-core/nanostring/pull/94) - Added nf-tests for local subworkflows normalize and quality_control.
+- [#94](https://github.com/nf-core/nanostring/pull/94) - Added nf-tests for local subworkflows `NORMALIZE` and `QUALITY_CONTROL`.
 - [#100](https://github.com/nf-core/nanostring/pull/100) - Added nf-tests for local module `NACHO_QC`.
 - [#101](https://github.com/nf-core/nanostring/pull/101) - Added nf-tests for local module `COMPUTE_GENE_SCORES`.
+- [#102](https://github.com/nf-core/nanostring/pull/102) - Added nf-tests for local module `CREATE_GENE_HEATMAP`.
 
 ### `Fixed`
 

modules/local/create_gene_heatmap/environment.yml

@@ -0,0 +1,12 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.4.4
+  - conda-forge::r-rlang=1.1.1
+  - conda-forge::r-fs=1.6.4
+  - bioconda::bioconductor-complexheatmap=2.14.0
+  - conda-forge::r-circlize=0.4.15
+  - conda-forge::r-yaml=2.3.8
+  - conda-forge::r-ragg=1.3.1

modules/local/create_gene_heatmap.nf → modules/local/create_gene_heatmap/main.nf

@@ -1,10 +1,8 @@
 process CREATE_GENE_HEATMAP {
     label 'process_single'
 
-    conda "r-dplyr=1.1.4 r-ggplot2=3.4.4 r-rlang=1.1.1 r-fs=1.6.2 bioconductor-complexheatmap=2.14.0 r-circlize=0.4.15 r-yaml=2.3.7 r-ragg=1.2.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-2e8e9d8610faa60024ab107974b3decf00600ddc:e99bc7b45df42fd6b3bd3e4019336741e068897b-0' :
-        'biocontainers/mulled-v2-2e8e9d8610faa60024ab107974b3decf00600ddc:e99bc7b45df42fd6b3bd3e4019336741e068897b-0' }"
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/bioconductor-complexheatmap_r-base_r-circlize_r-dplyr_pruned:58d1af3dbaeba617"
 
     input:
     path annotated_counts
@@ -27,8 +25,8 @@ process CREATE_GENE_HEATMAP {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
-        r-dplyr: \$(Rscript -e "library(tidyverse); cat(as.character(packageVersion('dplyr')))")
-        r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot')))")
+        r-dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))")
+        r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
         r-rlang: \$(Rscript -e "library(rlang); cat(as.character(packageVersion('rlang')))")
         bioconductor-ComplexHeatmap: \$(Rscript -e "library(ComplexHeatmap); cat(as.character(packageVersion('ComplexHeatmap')))")
         r-circlize: \$(Rscript -e "library(circlize); cat(as.character(packageVersion('circlize')))")

modules/local/create_gene_heatmap/meta.yml

@@ -0,0 +1,43 @@
+name: create_gene_heatmap
+description: Generate a gene count heatmap based on annotated and filtered gene counts data.
+keywords:
+  - bioinformatics tools
+  - data visualization
+  - gene heatmap
+tools:
+  - create_gene_heatmap:
+      description: |
+        The create_gene_heatmap module generates a heatmap of gene counts.
+        It supports gene selection via additional files and provides a log-transformed visualization of the data.
+input:
+  - - annotated_counts:
+        type: file
+        description: |
+          A tab-separated file containing annotated counts.
+        pattern: "*ENDO.tsv"
+  - - counts:
+        type: file
+        description: |
+          A tab-separated file containing counts data for genes, used when no gene set YAML is provided.
+        pattern: "*normalized_counts.tsv"
+  - - heatmap_genes_to_filter:
+        type: file
+        description: |
+          Path to yml file (list, one item per line) to specify which genes should be used for the gene-count heatmap.
+output:
+  - gene_heatmap:
+      - "*gene_heatmap_mqc.png":
+          type: file
+          description: |
+            A PNG image containing the gene count heatmap, suitable for inclusion in MultiQC reports.
+          pattern: "*gene_heatmap_mqc.png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing the software versions.
+          pattern: "versions.yml"
+authors:
+  - "@apeltzer"
+  - "@christopher-mohr"
+maintainers:
+  - "@nschcolnicov"

modules/local/create_gene_heatmap/tests/main.nf.test

@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test Process CREATE_GENE_HEATMAP"
+    script "../main.nf"
+    process "CREATE_GENE_HEATMAP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "CREATE_GENE_HEATMAP"
+
+    test("test profile") {
+
+        when {
+            process {
+                """
+                input[0] = file(params.pipelines_testdata_base_path + 'nanostring/modules_test_data/test_profile/counts_Norm_GEX_ENDO.tsv', checkIfExists: true )
+                input[1] = file(params.pipelines_testdata_base_path + 'nanostring/modules_test_data/test_profile/normalized_counts.tsv', checkIfExists: true )
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success},
+                { assert snapshot(
+                    process.out.gene_heatmap.collect { file(it).name }, //list unstable png files
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+    }
+}

modules/local/create_gene_heatmap/tests/main.nf.test.snap

@@ -0,0 +1,17 @@
+{
+    "test profile": {
+        "content": [
+            [
+                "gene_heatmap_mqc.png"
+            ],
+            [
+                "versions.yml:md5,ce9a0b1b0e476543f0a3ff5b93f6570b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-19T21:11:06.988380646"
+    }
+}

tests/test.nf.test.snap

@@ -10,14 +10,14 @@
                     "r-readr": "2.1.5"
                 },
                 "CREATE_GENE_HEATMAP": {
-                    "r-base": "4.3.2",
-                    "r-dplyr": null,
-                    "r-ggplot2": null,
-                    "r-rlang": "1.1.3",
-                    "bioconductor-ComplexHeatmap": "2.18.0",
+                    "r-base": "4.2.3",
+                    "r-dplyr": "1.1.4",
+                    "r-ggplot2": "3.4.4",
+                    "r-rlang": "1.1.1",
+                    "bioconductor-ComplexHeatmap": "2.14.0",
                     "r-circlize": "0.4.15",
-                    "r-yaml": "2.3.7",
-                    "r-fs": "1.6.2"
+                    "r-yaml": "2.3.8",
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
                     "r-base": "4.3.2",
@@ -115,6 +115,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T17:52:59.774386953"
+        "timestamp": "2024-11-19T21:23:55.334879021"
     }
-}
+}

tests/test_samples.nf.test.snap

@@ -10,14 +10,14 @@
                     "r-readr": "2.1.5"
                 },
                 "CREATE_GENE_HEATMAP": {
-                    "r-base": "4.3.2",
-                    "r-dplyr": null,
-                    "r-ggplot2": null,
-                    "r-rlang": "1.1.3",
-                    "bioconductor-ComplexHeatmap": "2.18.0",
+                    "r-base": "4.2.3",
+                    "r-dplyr": "1.1.4",
+                    "r-ggplot2": "3.4.4",
+                    "r-rlang": "1.1.1",
+                    "bioconductor-ComplexHeatmap": "2.14.0",
                     "r-circlize": "0.4.15",
-                    "r-yaml": "2.3.7",
-                    "r-fs": "1.6.2"
+                    "r-yaml": "2.3.8",
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
                     "r-base": "4.3.2",
@@ -115,6 +115,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T17:54:15.75754715"
+        "timestamp": "2024-11-19T21:24:55.10531256"
     }
-}
+}

tests/test_scores.nf.test.snap

@@ -21,14 +21,14 @@
                     "r-readr": "2.1.5"
                 },
                 "CREATE_GENE_HEATMAP": {
-                    "r-base": "4.3.2",
-                    "r-dplyr": null,
-                    "r-ggplot2": null,
-                    "r-rlang": "1.1.3",
-                    "bioconductor-ComplexHeatmap": "2.18.0",
+                    "r-base": "4.2.3",
+                    "r-dplyr": "1.1.4",
+                    "r-ggplot2": "3.4.4",
+                    "r-rlang": "1.1.1",
+                    "bioconductor-ComplexHeatmap": "2.14.0",
                     "r-circlize": "0.4.15",
-                    "r-yaml": "2.3.7",
-                    "r-fs": "1.6.2"
+                    "r-yaml": "2.3.8",
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
                     "r-base": "4.3.2",
@@ -141,6 +141,6 @@
             "nf-test": "0.9.0",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T17:57:05.905578506"
+        "timestamp": "2024-11-19T21:26:05.626984239"
     }
-}
+}