Merge pull request #99 from alanmmobbs93/update/create-test-nacho_nor…

…malize Update: create test nacho normalize
nf-core · Nov 21, 2024 · bc40764 · bc40764
2 parents 3e624d4 + d6f62a5
commit bc40764
Show file tree

Hide file tree

Showing 9 changed files with 105 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@ 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`.
+- [#99](https://github.com/nf-core/nanostring/pull/99) - Added nf-tests for local module `NACHO_NORMALIZE`.
 - [#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`.

diff --git a/modules/local/nacho/normalize/environment.yml b/modules/local/nacho/normalize/environment.yml
@@ -0,0 +1,9 @@
+channels:
+  - conda-forge
+dependencies:
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-fs=1.6.4
+  - conda-forge::r-ggplot2=3.4.4
+  - conda-forge::r-nacho=2.0.6
+  - conda-forge::r-readr=2.1.5
+  - conda-forge::r-tidyr=1.3.0
diff --git a/modules/local/nacho/normalize.nf → modules/local/nacho/normalize/main.nf b/modules/local/nacho/normalize.nf → modules/local/nacho/normalize/main.nf
@@ -1,10 +1,9 @@
 process NACHO_NORMALIZE {
+    tag "$sample_sheet"
     label 'process_single'
 
-    conda "r-nacho=2.0.6 r-dplyr=1.1.4 r-ggplot2=3.4.4 r-fs=1.6.4 r-readr=2.1.5 r-tidyr=1.3.0"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-9d27fb90b747ac2e521703d90daacce9cc1f33c5:98395a5d2e19da46499873cd2d76be73d6a0950d-0' :
-        'biocontainers/mulled-v2-9d27fb90b747ac2e521703d90daacce9cc1f33c5:98395a5d2e19da46499873cd2d76be73d6a0950d-0' }"
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:9bb487ee68105a77"
 
     input:
     path rcc_files
@@ -35,4 +34,22 @@ process NACHO_NORMALIZE {
         r-fs: \$(Rscript -e "library(fs); cat(as.character(packageVersion('fs')))")
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    touch normalized_counts.tsv
+    touch normalized_counts_wo_HKnorm.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        r-nacho: \$(Rscript -e "library(NACHO); cat(as.character(packageVersion('NACHO')))")
+        r-dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))")
+        r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot2')))")
+        r-tidyr: \$(Rscript -e "library(tidyr); cat(as.character(packageVersion('tidyr')))")
+        r-readr: \$(Rscript -e "library(readr); cat(as.character(packageVersion('readr')))")
+        r-fs: \$(Rscript -e "library(fs); cat(as.character(packageVersion('fs')))")
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/nacho/normalize/tests/main.nf.test b/modules/local/nacho/normalize/tests/main.nf.test
@@ -0,0 +1,33 @@
+nextflow_process {
+
+    name "Test Process NACHO_NORMALIZE"
+    script "../main.nf"
+    process "NACHO_NORMALIZE"
+    tag "modules"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                // RCC Files: Collect from sample sheet
+                input[0] = Channel.fromPath(params.pipelines_testdata_base_path + 'nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
+                    .splitCsv(header: true)
+                    .map { row -> row.RCC_FILE } // Select first column: path to file
+                    .collect()
+
+                // Sample sheet
+                input[1] = file(params.pipelines_testdata_base_path + 'nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/local/nacho/normalize/tests/main.nf.test.snap b/modules/local/nacho/normalize/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                ],
+                "1": [
+                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                ],
+                "2": [
+                    "versions.yml:md5,0b8556f7dd763f21894470ecc737ca3b"
+                ],
+                "normalized_counts": [
+                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                ],
+                "normalized_counts_wo_HK": [
+                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                ],
+                "versions": [
+                    "versions.yml:md5,0b8556f7dd763f21894470ecc737ca3b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-19T19:00:09.938938106"
+    }
+}
diff --git a/subworkflows/local/normalize/main.nf b/subworkflows/local/normalize/main.nf
@@ -2,7 +2,7 @@
 // Perform normalizations (currently using Nacho)
 //
 
-include { NACHO_NORMALIZE } from '../../../modules/local/nacho/normalize'
+include { NACHO_NORMALIZE } from '../../../modules/local/nacho/normalize/main'
 
 workflow NORMALIZE {
     take:

diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -20,13 +20,13 @@
                     "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-nacho": "2.0.6",
                     "r-dplyr": "1.1.4",
                     "r-ggplot2": "3.4.4",
                     "r-tidyr": "1.3.0",
                     "r-readr": "2.1.5",
-                    "r-fs": "1.6.2"
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_QC": {
                     "r-base": "4.3.3",

diff --git a/tests/test_samples.nf.test.snap b/tests/test_samples.nf.test.snap
@@ -20,13 +20,13 @@
                     "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-nacho": "2.0.6",
                     "r-dplyr": "1.1.4",
                     "r-ggplot2": "3.4.4",
                     "r-tidyr": "1.3.0",
                     "r-readr": "2.1.5",
-                    "r-fs": "1.6.2"
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_QC": {
                     "r-base": "4.3.3",

diff --git a/tests/test_scores.nf.test.snap b/tests/test_scores.nf.test.snap
@@ -31,13 +31,13 @@
                     "r-fs": "1.6.4"
                 },
                 "NACHO_NORMALIZE": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-nacho": "2.0.6",
                     "r-dplyr": "1.1.4",
                     "r-ggplot2": "3.4.4",
                     "r-tidyr": "1.3.0",
                     "r-readr": "2.1.5",
-                    "r-fs": "1.6.2"
+                    "r-fs": "1.6.4"
                 },
                 "NACHO_QC": {
                     "r-base": "4.3.3",
@@ -138,9 +138,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
+            "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-19T21:26:05.626984239"
+        "timestamp": "2024-11-20T20:01:05.948521351"
     }
-}
+}