New Module: NACHO_NORMALISE

modules/nf-core/nacho/normalise/environment.yml

@@ -1,5 +1,4 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
 dependencies:

modules/nf-core/nacho/normalise/main.nf

@@ -1,15 +1,15 @@
 nextflow.enable.moduleBinaries = true
 
 process NACHO_NORMALISE {
-    tag "$sample_sheet"
+    tag "${meta.id}"
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
     container 'community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:033bc017f5f36b6d'
 
     input:
-    path rcc_files, stageAs: "input/*"
-    path sample_sheet
+    tuple val(meta) , path(rcc_files, stageAs: "input/*")
+    tuple val(meta2), path(sample_sheet)
 
     output:
     path "*normalized_counts.tsv"          , emit: normalized_counts
@@ -22,7 +22,10 @@ process NACHO_NORMALISE {
     script:
     def args = task.ext.args ?: ''
     """
-    nacho_norm.R --input_rcc_path input --input_samplesheet ${sample_sheet} $args
+    nacho_norm.R \\
+        --input_rcc_path input \\
+        $args \\
+        --input_samplesheet ${sample_sheet}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/nacho/normalise/meta.yml

@@ -1,5 +1,4 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: nacho_normalise
 description: |
   NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.
@@ -22,8 +21,8 @@ tools:
       homepage: https://github.com/mcanouil/NACHO
       documentation: https://cran.r-project.org/web/packages/NACHO/vignettes/NACHO.html
       doi: "doi:10.1093/bioinformatics/btz647"
-      licence: GPL-3.0 license
-      identifier: biotools:nacho
+      licence: [ "GPL-3.0" ]
+      identifier: ""
 
 input:
   - - rcc_files:
@@ -59,6 +58,6 @@ output:
         pattern: "versions.yml"
 
 authors:
-  - Mickaël Canouil, Gerard A. Bouland, Amélie Bonnefond, Philippe Froguel, Leen Hart, and Roderick Slieker.
+  - "@alanmobbs93"
 maintainers:
-  -
+  - "@alanmobbs93"

modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R

@@ -51,12 +51,13 @@ input_rcc_path    <- opt$input_rcc_path
 input_samplesheet <- opt$input_samplesheet
 norm_method       <- opt$norm_method
 
-#Create filelist for NachoQC
+# Create filelist for NachoQC
 
 list_of_rccs <- dir_ls(path = input_rcc_path, glob = "*.RCC")
 print(list_of_rccs)
 
-####RealCode####
+# Core Code
+## Read data
 nacho_data <- load_rcc(data_directory = input_rcc_path,
                     ssheet_csv = input_samplesheet,
                     id_colname = "RCC_FILE_NAME",
@@ -75,16 +76,17 @@ get_counts <- function(
     tidyr::pivot_wider(names_from = "RCC_FILE_NAME", values_from = "Count_Norm")
 }
 
-#Write out normalized counts
+## Write out normalized counts
 norm_counts <- as.data.frame(get_counts(nacho_data))
 write_tsv(norm_counts, file = "normalized_counts.tsv")
 
-#Write out non-hk normalized counts too
+## Create non-hk normalized counts too
 nacho_data_no_hk <- load_rcc(data_directory = input_rcc_path,
     ssheet_csv = input_samplesheet,
     id_colname = "RCC_FILE_NAME",
     normalisation_method = norm_method,
     housekeeping_norm = FALSE)
 
+## Export non-hk tables
 norm_counts_without_hks <- as.data.frame(get_counts(nacho_data_no_hk))
 write_tsv(norm_counts_without_hks, file = "normalized_counts_wo_HKnorm.tsv")

modules/nf-core/nacho/normalise/tests/main.nf.test

@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test nacho/normalise
 nextflow_process {
 
     name "Test Process NACHO_NORMALISE"
@@ -12,7 +10,7 @@ nextflow_process {
     tag "nacho"
     tag "nacho/normalise"
 
-    test("Should run without failures") {
+    test("Salmon - RCC files") {
 
         when {
             params {
@@ -21,13 +19,58 @@ nextflow_process {
             process {
                 """
                 // RCC Files: Collect from sample sheet
-                input[0] = Channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
-                    .splitCsv(header: true)
-                    .map { row -> row.RCC_FILE } // Select first column: path to file
-                    .collect()
+                input[0] =
+                    Channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
+                        .splitCsv( header: true )
+                        .map { row -> return file(row.RCC_FILE, checkIfExists: true) } // Select first column: path to file // Select first column: path to file
+                        .collect()
+                        .map{ files ->
+                            tuple( [id: 'test'], files ) // Add meta component
+                        }
+
+
+                // Sample sheet
+                input[1] = Channel.of( [
+                        [ id: 'test_samplesheet'],
+                        [ file('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true) ]
+                    ] )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("Salmon - RCC files - Stub") {
+
+        options "-stub"
+        when {
+            params {
+                module_args = '--norm_method "GEO"'
+            }
+            process {
+                """
+                // RCC Files: Collect from sample sheet
+                input[0] =
+                    Channel.fromPath('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
+                        .splitCsv( header: true )
+                        .map { row -> return file(row.RCC_FILE, checkIfExists: true) } // Select first column: path to file // Select first column: path to file
+                        .collect()
+                        .map{ files ->
+                            tuple( [id: 'test'], files ) // Add meta component
+                        }
 
                 // Sample sheet
-                input[1] = file('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true)
+                input[1] =
+                    Channel.of( [
+                        [id: 'test_samplesheet'],
+                        [ file('https://raw.githubusercontent.com/nf-core/test-datasets/nanostring/samplesheets/samplesheet_test.csv', checkIfExists: true) ]
+                    ] )
                 """
             }
         }

modules/nf-core/nacho/normalise/tests/main.nf.test.snap

@@ -1,5 +1,34 @@
 {
-    "Should run without failures": {
+    "Salmon - RCC files - Stub": {
+        "content": [
+            {
+                "0": [
+                    "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "2": [
+                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                ],
+                "normalized_counts": [
+                    "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "normalized_counts_wo_HK": [
+                    "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-27T15:13:12.044326701"
+    },
+    "Salmon - RCC files": {
         "content": [
             {
                 "0": [
@@ -26,6 +55,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-26T20:12:23.648098726"
+        "timestamp": "2024-11-27T15:12:49.870804363"
     }
 }