resolve conflicts

Author: alanmmobbs93

CHANGELOG.md

@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#82](https://github.com/nf-core/nanostring/pull/82) - Updated to nf-core template 3.0.2
 - [#95](https://github.com/nf-core/nanostring/pull/95) - Add pipeline level nf-tests.
 - [#96](https://github.com/nf-core/nanostring/pull/96) - Remove timestamp suffix from nacho_norm.R and write_out_prepared_gex.R
+- [#99](https://github.com/nf-core/nanostring/pull/99) - Add nf-test for local module nacho_normalize.
 
 ### `Dependencies`
 

modules/local/nacho/normalize/environment.yml

@@ -0,0 +1,9 @@
+channels:
+  - conda-forge
+dependencies:
+  - conda-forge::r-nacho=2.0.6
+  - conda-forge::r-dplyr=1.2.2
+  - conda-forge::r-ggplot2=3.4.4
+  - conda-forge::r-fs=1.6.2
+  - conda-forge::r-readr=2.1.5
+  - conda-forge::r-tidyr=1.3.0

modules/local/nacho/normalize.nf modules/local/nacho/normalize/main.nfmodules/local/nacho/normalize.nf renamed to modules/local/nacho/normalize/main.nf

@@ -1,7 +1,8 @@
 process NACHO_NORMALIZE {
+    tag '$sample_sheet'
     label 'process_single'
 
-    conda "r-nacho=2.0.6 r-dplyr=1.2.2 r-ggplot2=3.4.4 r-fs=1.6.2 r-readr=2.1.5 r-tidyr=1.3.0"
+    conda "${moduleDir}/environment.yml"
     container "${ 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' }"
@@ -35,4 +36,22 @@ 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
+    """
 }

modules/local/nacho/normalize/tests/main.nf.test

@@ -0,0 +1,35 @@
+nextflow_process {
+
+    name "Test Process NACHO_NORMALIZE"
+    script "../main.nf"
+    process "NACHO_NORMALIZE"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
+                input  = params.pipelines_testdata_base_path + 'nanostring/samplesheets/samplesheet_test.csv'
+            }
+            process {
+                """
+                // RCC Files: Collect from samplesheet
+                input[0] = Channel.fromPath(params.input, checkIfExists: true)
+                    .splitCsv(header: true)
+                    .map { row -> row.RCC_FILE } // Select first column: path to file
+                    .collect()
+
+                // Sample sheet
+                input[1] = file(params.input, checkIfExists: true)
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

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,dd0bb0b151596e1316c29a51f38f5a2e"
+                ],
+                "normalized_counts": [
+                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                ],
+                "normalized_counts_wo_HK": [
+                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                ],
+                "versions": [
+                    "versions.yml:md5,dd0bb0b151596e1316c29a51f38f5a2e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-19T15:00:56.669733561"
+    }
+}

subworkflows/local/normalize.nf

@@ -0,0 +1,19 @@
+//
+// Perform normalizations (currently using Nacho)
+//
+
+include { NACHO_NORMALIZE } from '../../modules/local/nacho/normalize/main'
+
+workflow NORMALIZE {
+    take:
+    counts      // channel: [ meta, path(rcc) ]
+    samplesheet // file: /path/to/samplesheet.csv
+
+    main:
+    NACHO_NORMALIZE ( counts, samplesheet )
+
+    emit:
+    normalized_counts = NACHO_NORMALIZE.out.normalized_counts                              // channel: [ val(meta), [ counts ] ]
+    normalized_counts_wo_HK = NACHO_NORMALIZE.out.normalized_counts_wo_HK  // channel: [ samplesheet.valid.csv ]
+    versions = NACHO_NORMALIZE.out.versions // channel: [ versions.yml ]
+}

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: