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nf-core · Nov 22, 2024 · e803009 · e803009
2 parents 9d910ea + c20d880
commit e803009
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Showing 9 changed files with 109 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#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`.
+- [#103](https://github.com/nf-core/nanostring/pull/103) - Added nf-tests for local module `CREATE_ANNOTATED_TABLES`.
 - [#104](https://github.com/nf-core/nanostring/pull/104) - Update all nf-core modules and subworkflows.
 
 ### `Fixed`

diff --git a/modules/local/create_annotated_tables/environment.yml b/modules/local/create_annotated_tables/environment.yml
@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+dependencies:
+  - conda-forge::r-dplyr=1.1.4
+  - conda-forge::r-ggplot2=3.4.4
+  - conda-forge::r-readr=2.1.5
+  - conda-forge::r-stringr=1.5.0
+  - conda-forge::r-tidyr=1.3.0
diff --git a/modules/local/create_annotated_tables.nf → ...les/local/create_annotated_tables/main.nf b/modules/local/create_annotated_tables.nf → ...les/local/create_annotated_tables/main.nf
@@ -1,10 +1,9 @@
 process CREATE_ANNOTATED_TABLES {
+    tag "$sample_sheet"
     label 'process_single'
 
-    conda "r-tidyr=1.3.0 r-ggplot2=3.4.4 r-dplyr=1.1.4 r-stringr=1.5.0 r-readr=2.1.5"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-5ff8b00c2d7f6173e034c115dfe295627ff99689:beb0ad5f49ec2904f79edffacd41bba38492e881-0' :
-        'biocontainers/mulled-v2-5ff8b00c2d7f6173e034c115dfe295627ff99689:beb0ad5f49ec2904f79edffacd41bba38492e881-0' }"
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/r-dplyr_r-ggplot2_r-readr_r-stringr_r-tidyr:44c4e4fe69e11c2f"
 
     input:
     path counts
@@ -32,5 +31,20 @@ process CREATE_ANNOTATED_TABLES {
         r-readr: \$(Rscript -e "library(readr); cat(as.character(packageVersion('readr')))")
     END_VERSIONS
     """
-}
 
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    touch ENDO.tsv
+    touch HK.tsv
+    touch mqc.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
+        r-ggplot2: \$(Rscript -e "library(ggplot2); cat(as.character(packageVersion('ggplot')))")
+        r-dplyr: \$(Rscript -e "library(dplyr); cat(as.character(packageVersion('dplyr')))")
+        r-readr: \$(Rscript -e "library(readr); cat(as.character(packageVersion('readr')))")
+    END_VERSIONS
+    """
+}
diff --git a/modules/local/create_annotated_tables/tests/main.nf.test b/modules/local/create_annotated_tables/tests/main.nf.test
@@ -0,0 +1,31 @@
+nextflow_process {
+
+    name "Test Process CREATE_ANNOTATED_TABLES"
+    script "../main.nf"
+    process "CREATE_ANNOTATED_TABLES"
+    tag "module"
+
+    test("Should run without failures") {
+
+        when {
+            process {
+                """
+                // Normalized file
+                input[0] = file(params.pipelines_testdata_base_path + 'nanostring/modules_test_data/test_profile/normalized_counts.tsv', checkIfExists: true)
+
+                // 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/create_annotated_tables/tests/main.nf.test.snap b/modules/local/create_annotated_tables/tests/main.nf.test.snap
@@ -0,0 +1,43 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    "counts_Norm_GEX_ENDO.tsv:md5,5992886680cb6fc6f3e901e79752d544"
+                ],
+                "1": [
+                    "counts_Norm_GEX_HK.tsv:md5,9d8a0503df864a82990648348131be21"
+                ],
+                "2": [
+                    [
+                        "Norm_GEX_ENDO_mqc.tsv:md5,5992886680cb6fc6f3e901e79752d544",
+                        "Norm_GEX_HK_mqc.tsv:md5,9d8a0503df864a82990648348131be21"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,43b871def59fb08862ac85e636101fe5"
+                ],
+                "annotated_data_mqc": [
+                    [
+                        "Norm_GEX_ENDO_mqc.tsv:md5,5992886680cb6fc6f3e901e79752d544",
+                        "Norm_GEX_HK_mqc.tsv:md5,9d8a0503df864a82990648348131be21"
+                    ]
+                ],
+                "annotated_endo_data": [
+                    "counts_Norm_GEX_ENDO.tsv:md5,5992886680cb6fc6f3e901e79752d544"
+                ],
+                "annotated_hk_data": [
+                    "counts_Norm_GEX_HK.tsv:md5,9d8a0503df864a82990648348131be21"
+                ],
+                "versions": [
+                    "versions.yml:md5,43b871def59fb08862ac85e636101fe5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-20T14:10:50.997813905"
+    }
+}
diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap
@@ -4,7 +4,7 @@
             5,
             {
                 "CREATE_ANNOTATED_TABLES": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-ggplot2": null,
                     "r-dplyr": "1.1.4",
                     "r-readr": "2.1.5"
@@ -112,4 +112,4 @@
         },
         "timestamp": "2024-11-22T14:03:55.044702369"
     }
-}
+}
diff --git a/tests/test_samples.nf.test.snap b/tests/test_samples.nf.test.snap
@@ -4,7 +4,7 @@
             5,
             {
                 "CREATE_ANNOTATED_TABLES": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-ggplot2": null,
                     "r-dplyr": "1.1.4",
                     "r-readr": "2.1.5"
@@ -114,4 +114,4 @@
         },
         "timestamp": "2024-11-22T14:04:43.919125465"
     }
-}
+}
diff --git a/tests/test_scores.nf.test.snap b/tests/test_scores.nf.test.snap
@@ -15,7 +15,7 @@
                     "r-matrixstats": null
                 },
                 "CREATE_ANNOTATED_TABLES": {
-                    "r-base": "4.3.2",
+                    "r-base": "4.3.3",
                     "r-ggplot2": null,
                     "r-dplyr": "1.1.4",
                     "r-readr": "2.1.5"
@@ -140,4 +140,4 @@
         },
         "timestamp": "2024-11-22T14:06:23.244531229"
     }
-}
+}
diff --git a/workflows/nanostring.nf b/workflows/nanostring.nf
@@ -91,7 +91,7 @@ workflow NANOSTRING {
     // MODULE: Annotate normalized counts with metadata from the samplesheet
     //
     CREATE_ANNOTATED_TABLES (
-        NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK),
+        NORMALIZE.out.normalized_counts.mix(NORMALIZE.out.normalized_counts_wo_HK).toSortedList().flatten(),
         samplesheet_path
     )
     ch_versions      = ch_versions.mix(CREATE_ANNOTATED_TABLES.out.versions)