From 51c85636246f55803e353c7487e7c00a0d0fc2f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 13:35:29 +0000
Subject: [PATCH 01/17] Create module

---
 .gitignore                                    |  1 +
 .../nf-core/nacho/normalise/environment.yml   | 12 +++
 modules/nf-core/nacho/normalise/main.nf       | 72 +++++++++++++++
 modules/nf-core/nacho/normalise/meta.yml      | 58 ++++++++++++
 .../normalise/resources/usr/bin/nacho_norm.R  | 89 +++++++++++++++++++
 .../nacho/normalise/tests/main.nf.test        | 43 +++++++++
 .../nacho/normalise/tests/main.nf.test.snap   | 31 +++++++
 .../nacho/normalise/tests/nextflow.config     |  5 ++
 8 files changed, 311 insertions(+)
 create mode 100644 modules/nf-core/nacho/normalise/environment.yml
 create mode 100644 modules/nf-core/nacho/normalise/main.nf
 create mode 100644 modules/nf-core/nacho/normalise/meta.yml
 create mode 100755 modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
 create mode 100644 modules/nf-core/nacho/normalise/tests/main.nf.test
 create mode 100644 modules/nf-core/nacho/normalise/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/nacho/normalise/tests/nextflow.config

diff --git a/.gitignore b/.gitignore
index 34cd784c6ee..5063679f104 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,3 +15,4 @@ test_output/
 tests/data/
 work/
 .github/CODEOWNERS-tmp
+install_r.sh
diff --git a/modules/nf-core/nacho/normalise/environment.yml b/modules/nf-core/nacho/normalise/environment.yml
new file mode 100644
index 00000000000..f7cc5f665f7
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/environment.yml
@@ -0,0 +1,12 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+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
+  - conda-forge::r-optparse=1.6.0
diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
new file mode 100644
index 00000000000..11fd6eeb106
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/main.nf
@@ -0,0 +1,72 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+nextflow.enable.moduleBinaries = true
+
+process NACHO_NORMALISE {
+    tag "$sample_sheet"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:9bb487ee68105a77"
+
+    input:
+    path rcc_files, stageAs: "input/*"
+    path sample_sheet
+
+    output:
+    path "*normalized_counts.tsv"          , emit: normalized_counts
+    path "*normalized_counts_wo_HKnorm.tsv", emit: normalized_counts_wo_HK
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    nacho_norm.R --input_rcc_path input --input_samplesheet ${sample_sheet} $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${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
+    """
+
+    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/nf-core/nacho/normalise/meta.yml b/modules/nf-core/nacho/normalise/meta.yml
new file mode 100644
index 00000000000..cc4af100e61
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/meta.yml
@@ -0,0 +1,58 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "nacho_normalise"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "nacho":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence: 
+      identifier: biotools:NACHO
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  #
+  ## TODO nf-core: Delete / customise this example input
+    - bam:
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+          
+
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+  - bam:
+  #
+  ## TODO nf-core: Delete / customise this example output
+    - "*.bam":
+        type: file
+        description: Sorted BAM/CRAM/SAM file
+        pattern: "*.{bam,cram,sam}"
+        ontologies:
+          - edam: "http://edamontology.org/format_25722"
+          - edam: "http://edamontology.org/format_2573"
+          - edam: "http://edamontology.org/format_3462"
+          
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@alanmmobbs93"
+maintainers:
+  - "@alanmmobbs93"
diff --git a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
new file mode 100755
index 00000000000..a35de5b7768
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
@@ -0,0 +1,89 @@
+#!/usr/bin/env Rscript
+library(optparse)
+library(dplyr)
+library(ggplot2)
+library(fs)
+library(NACHO)
+library(readr)
+library(tidyr)
+
+# Parse Arguments
+norm_methods <- c("GLM", "GEO")
+option_list <- list(
+    make_option(
+        c("--input_rcc_path"),
+        type = "character",
+        default = "./" ,
+        help = "Path to the folder that contains the RCC input file(s)",
+        metavar = "character"),
+    make_option(
+        c("--input_samplesheet"),
+        type = "character",
+        default = NULL ,
+        help = "Path to the sample sheet file",
+        metavar = "character"),
+    make_option(
+        c("--norm_method"),
+        type = "character",
+        default = "GLM",
+        help = paste0("Normalization method. One of ", paste(norm_methods, collapse = " "), paste = " "),
+        metavar = "character")
+)
+
+# Parse the command-line arguments
+opt <- parse_args(OptionParser(option_list = option_list))
+
+# Validate mandatory arguments
+if (is.null(opt$input_rcc_path)) {
+    stop("Error: The --input_rcc_path parameter is mandatory and must be specified.")
+}
+
+if (is.null(opt$input_samplesheet)) {
+    stop("Error: The --input_samplesheet parameter is mandatory and must be specified.")
+}
+
+# Validate that --norm_method is one of the allowed values
+if (!(opt$norm_method %in% norm_methods <- c("GLM", "GEO"))) {
+    stop(paste("Error: The --norm_method parameter must be one of:", paste(norm_methods, collapse = " ")))
+}
+
+input_rcc_path <- opt$input_rcc_path
+input_samplesheet <- opt$input_samplesheet
+norm_method <- opt$norm_method
+
+#Create filelist for NachoQC
+
+list_of_rccs <- dir_ls(path = input_rcc_path, glob = "*.RCC", full.names = TRUE)
+
+####RealCode####
+nacho_data <- load_rcc(data_directory = input_rcc_path,
+                    ssheet_csv = input_samplesheet,
+                    id_colname = "RCC_FILE_NAME",
+                    normalisation_method = norm_method)
+
+output_base <- "./"
+
+get_counts <- function(
+    nacho,
+    codeclass = "Endogenous",
+    rownames = "RCC_FILE_NAME",
+    colnames = c("Name", "Accession")
+) {
+    nacho[["nacho"]] %>%
+    dplyr::select(c("RCC_FILE_NAME", "Name", "Count_Norm", "CodeClass")) %>%
+    tidyr::pivot_wider(names_from = "RCC_FILE_NAME", values_from = "Count_Norm")
+}
+
+#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
+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)
+
+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")
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalise/tests/main.nf.test
new file mode 100644
index 00000000000..dcb2ee297f6
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test
@@ -0,0 +1,43 @@
+// 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"
+    script "../main.nf"
+    process "NACHO_NORMALISE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "nacho"
+    tag "nacho/normalise"
+
+    test("Should run without failures") {
+
+        when {
+            params {
+                module_args = '--norm_method "GLM"'
+            }
+            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()
+
+                // Sample sheet
+                input[1] = 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() }
+            )
+        }
+    }
+
+}
\ No newline at end of file
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
new file mode 100644
index 00000000000..328b619b96b
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
@@ -0,0 +1,31 @@
+{
+    "Should run without failures": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "normalized_counts": [
+                    
+                ],
+                "normalized_counts_wo_HK": [
+                    
+                ],
+                "versions": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-11-26T12:25:34.208864197"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/nacho/normalise/tests/nextflow.config b/modules/nf-core/nacho/normalise/tests/nextflow.config
new file mode 100644
index 00000000000..918ae6f89ed
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'NACHO_NORMALISE' {
+        ext.args = params.module_args
+    }
+}

From 3c5386ee09061dd6e96b442dacc29597ed723f5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 20:01:44 +0000
Subject: [PATCH 02/17] parse arguments on module R script

---
 modules/nf-core/nacho/normalise/main.nf       | 20 +++----------------
 .../normalise/resources/usr/bin/nacho_norm.R  |  9 +++++----
 2 files changed, 8 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
index 11fd6eeb106..98397b64784 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/modules/nf-core/nacho/normalise/main.nf
@@ -1,19 +1,3 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
 nextflow.enable.moduleBinaries = true
 
 process NACHO_NORMALISE {
@@ -21,7 +5,7 @@ process NACHO_NORMALISE {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:9bb487ee68105a77"
+    container 'community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:2d777db141950c99'
 
     input:
     path rcc_files, stageAs: "input/*"
@@ -49,6 +33,7 @@ process NACHO_NORMALISE {
         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')))")
+        r-optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
     END_VERSIONS
     """
 
@@ -67,6 +52,7 @@ process NACHO_NORMALISE {
         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')))")
+        r-optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
index a35de5b7768..dc424d852c6 100755
--- a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
+++ b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
@@ -43,17 +43,18 @@ if (is.null(opt$input_samplesheet)) {
 }
 
 # Validate that --norm_method is one of the allowed values
-if (!(opt$norm_method %in% norm_methods <- c("GLM", "GEO"))) {
+if (!(opt$norm_method %in% norm_methods)) {
     stop(paste("Error: The --norm_method parameter must be one of:", paste(norm_methods, collapse = " ")))
 }
 
-input_rcc_path <- opt$input_rcc_path
+input_rcc_path    <- opt$input_rcc_path
 input_samplesheet <- opt$input_samplesheet
-norm_method <- opt$norm_method
+norm_method       <- opt$norm_method
 
 #Create filelist for NachoQC
 
-list_of_rccs <- dir_ls(path = input_rcc_path, glob = "*.RCC", full.names = TRUE)
+list_of_rccs <- dir_ls(path = input_rcc_path, glob = "*.RCC")
+print(list_of_rccs)
 
 ####RealCode####
 nacho_data <- load_rcc(data_directory = input_rcc_path,

From 713eb78bc0e7ae6cf7150faccddea1eefcce3e5a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 20:01:56 +0000
Subject: [PATCH 03/17] update meta info

---
 modules/nf-core/nacho/normalise/meta.yml | 90 +++++++++++++-----------
 1 file changed, 48 insertions(+), 42 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/meta.yml b/modules/nf-core/nacho/normalise/meta.yml
index cc4af100e61..d9c30082555 100644
--- a/modules/nf-core/nacho/normalise/meta.yml
+++ b/modules/nf-core/nacho/normalise/meta.yml
@@ -1,58 +1,64 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
-name: "nacho_normalise"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+name: nacho_normalise
+description: |
+  NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.
+  NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes.
+  Each barcode is assigned a mRNA/miRNA, which can be counted after bonding with its target.
+  As a result each count of a specific barcode represents the presence of its target mRNA/miRNA.
 keywords:
-  - sort
-  - example
-  - genomics
+  - nacho
+  - nanostring
+  - mRNA
+  - miRNA
+  - qc
 tools:
-  - "nacho":
-      ## TODO nf-core: Add a description and other details for the software below
-      description: ""
-      homepage: ""
-      documentation: ""
-      tool_dev_url: ""
-      doi: ""
-      licence: 
-      identifier: biotools:NACHO
+  - NACHO:
+      description: |
+        R package that uses two main functions to summarize and visualize NanoString RCC files,
+        namely: `load_rcc()` and `visualise()`. It also includes a function `normalise()`, which (re)calculates
+        sample specific size factors and normalises the data.
+        For more information `vignette("NACHO")` and `vignette("NACHO-analysis")`
+      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
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  #
-  ## TODO nf-core: Delete / customise this example input
-    - bam:
-        type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-          
+  - - rcc_files:
+      type: file
+      description: |
+        List of RCC files for all samples, which are direct outputs from NanoString runs
+      pattern: "*.RCC"
+  - - sample_sheet:
+      type: "file"
+      pattern: "*.csv"
+      description: |
+        Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  - bam:
-  #
-  ## TODO nf-core: Delete / customise this example output
-    - "*.bam":
+  - normalized_counts:
+    - "normalized_counts.tsv":
+        type: file
+        description: |
+          Tab-separated file with gene normalized counts for the samples
+        pattern: "*normalized_counts.tsv"
+
+  - normalized_counts_wo_HK:
+    - "normalized_counts_wo_HKnorm.tsv":
         type: file
-        description: Sorted BAM/CRAM/SAM file
-        pattern: "*.{bam,cram,sam}"
-        ontologies:
-          - edam: "http://edamontology.org/format_25722"
-          - edam: "http://edamontology.org/format_2573"
-          - edam: "http://edamontology.org/format_3462"
-          
+        description: |
+          Tab-separated file with gene normalized counts for the samples, without housekeeping genes.
+        pattern: "*normalized_counts_wo_HKnorm.tsv"
   - versions:
     - "versions.yml":
         type: file
-        description: File containing software versions
+        description: |
+          File containing software versions
         pattern: "versions.yml"
 
 authors:
-  - "@alanmmobbs93"
+  - Mickaël Canouil, Gerard A. Bouland, Amélie Bonnefond, Philippe Froguel, Leen Hart, and Roderick Slieker.
 maintainers:
-  - "@alanmmobbs93"
+  -

From 290b53f3be8a5188a2f050a273740a2a72917a31 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 20:02:19 +0000
Subject: [PATCH 04/17] update nf-test

---
 modules/nf-core/nacho/normalise/tests/main.nf.test |  2 +-
 .../nacho/normalise/tests/main.nf.test.snap        | 14 +++++++-------
 modules/nf-core/nacho/normalise/tests/test.tap     |  2 ++
 3 files changed, 10 insertions(+), 8 deletions(-)
 create mode 100644 modules/nf-core/nacho/normalise/tests/test.tap

diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalise/tests/main.nf.test
index dcb2ee297f6..4de31dabfc5 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test
@@ -16,7 +16,7 @@ nextflow_process {
 
         when {
             params {
-                module_args = '--norm_method "GLM"'
+                module_args = '--norm_method "GEO"'
             }
             process {
                 """
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
index 328b619b96b..20de39a1e13 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
@@ -3,22 +3,22 @@
         "content": [
             {
                 "0": [
-                    
+                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
                 ],
                 "1": [
-                    
+                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                 ],
                 "2": [
-                    
+                    "versions.yml:md5,48b34cd3436038e6e80c7f92880be9f1"
                 ],
                 "normalized_counts": [
-                    
+                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
                 ],
                 "normalized_counts_wo_HK": [
-                    
+                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                 ],
                 "versions": [
-                    
+                    "versions.yml:md5,48b34cd3436038e6e80c7f92880be9f1"
                 ]
             }
         ],
@@ -26,6 +26,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-26T12:25:34.208864197"
+        "timestamp": "2024-11-26T14:56:01.696817905"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/nacho/normalise/tests/test.tap b/modules/nf-core/nacho/normalise/tests/test.tap
new file mode 100644
index 00000000000..c8041c24064
--- /dev/null
+++ b/modules/nf-core/nacho/normalise/tests/test.tap
@@ -0,0 +1,2 @@
+1..1
+ok 1 Test Process NACHO_NORMALISE: Should run without failures

From 69373fdad0c4c6ac0b202fc58fa552871df8f2f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 20:52:02 +0000
Subject: [PATCH 05/17] update snaps after upgrading versions file

---
 modules/nf-core/nacho/normalise/environment.yml         | 2 +-
 modules/nf-core/nacho/normalise/main.nf                 | 2 +-
 modules/nf-core/nacho/normalise/tests/main.nf.test.snap | 6 +++---
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/environment.yml b/modules/nf-core/nacho/normalise/environment.yml
index f7cc5f665f7..d22767a170a 100644
--- a/modules/nf-core/nacho/normalise/environment.yml
+++ b/modules/nf-core/nacho/normalise/environment.yml
@@ -9,4 +9,4 @@ dependencies:
   - conda-forge::r-nacho=2.0.6
   - conda-forge::r-readr=2.1.5
   - conda-forge::r-tidyr=1.3.0
-  - conda-forge::r-optparse=1.6.0
+  - conda-forge::r-optparse=1.7.5
diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
index 98397b64784..87c26de0300 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/modules/nf-core/nacho/normalise/main.nf
@@ -5,7 +5,7 @@ process NACHO_NORMALISE {
     label 'process_single'
 
     conda "${moduleDir}/environment.yml"
-    container 'community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:2d777db141950c99'
+    container 'community.wave.seqera.io/library/r-dplyr_r-fs_r-ggplot2_r-nacho_pruned:033bc017f5f36b6d'
 
     input:
     path rcc_files, stageAs: "input/*"
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
index 20de39a1e13..5660052b028 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
@@ -9,7 +9,7 @@
                     "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                 ],
                 "2": [
-                    "versions.yml:md5,48b34cd3436038e6e80c7f92880be9f1"
+                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
                 ],
                 "normalized_counts": [
                     "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
@@ -18,7 +18,7 @@
                     "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                 ],
                 "versions": [
-                    "versions.yml:md5,48b34cd3436038e6e80c7f92880be9f1"
+                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
                 ]
             }
         ],
@@ -26,6 +26,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-26T14:56:01.696817905"
+        "timestamp": "2024-11-26T20:12:23.648098726"
     }
 }
\ No newline at end of file

From ec020a1da54934cfbd51940f932d6d58916cfa00 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Tue, 26 Nov 2024 20:55:17 +0000
Subject: [PATCH 06/17] update snaps after upgrading versions file

---
 .gitignore | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 5063679f104..34cd784c6ee 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,4 +15,3 @@ test_output/
 tests/data/
 work/
 .github/CODEOWNERS-tmp
-install_r.sh

From 2e306bb0e492fe8d9c013e55072911601757b145 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 15:19:29 +0000
Subject: [PATCH 07/17] add stub test, meta components and update names

---
 modules/nf-core/nacho/normalise/main.nf       | 11 ++--
 .../normalise/resources/usr/bin/nacho_norm.R  | 10 ++--
 .../nacho/normalise/tests/main.nf.test        | 59 ++++++++++++++++---
 .../nacho/normalise/tests/main.nf.test.snap   | 33 ++++++++++-
 .../nf-core/nacho/normalise/tests/test.tap    |  2 -
 5 files changed, 95 insertions(+), 20 deletions(-)
 delete mode 100644 modules/nf-core/nacho/normalise/tests/test.tap

diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
index 87c26de0300..495551473ec 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/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
     "${task.process}":
diff --git a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
index dc424d852c6..53899126a3b 100755
--- a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
+++ b/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
@@ -51,12 +51,13 @@ input_rcc_path    <- opt$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")
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalise/tests/main.nf.test
index 4de31dabfc5..d14b0873006 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test
+++ b/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) ]
+                    ] )
                 """
             }
         }
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
index 5660052b028..6d242b1e833 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
+++ b/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"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/nacho/normalise/tests/test.tap b/modules/nf-core/nacho/normalise/tests/test.tap
deleted file mode 100644
index c8041c24064..00000000000
--- a/modules/nf-core/nacho/normalise/tests/test.tap
+++ /dev/null
@@ -1,2 +0,0 @@
-1..1
-ok 1 Test Process NACHO_NORMALISE: Should run without failures

From 32b8b2b530b51c6afa92d391f30f243ac168bac1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 15:19:56 +0000
Subject: [PATCH 08/17] remove comments from ymls

---
 modules/nf-core/nacho/normalise/environment.yml | 1 -
 modules/nf-core/nacho/normalise/meta.yml        | 9 ++++-----
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/environment.yml b/modules/nf-core/nacho/normalise/environment.yml
index d22767a170a..a06ce44af9c 100644
--- a/modules/nf-core/nacho/normalise/environment.yml
+++ b/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:
diff --git a/modules/nf-core/nacho/normalise/meta.yml b/modules/nf-core/nacho/normalise/meta.yml
index d9c30082555..2eccbeaf3eb 100644
--- a/modules/nf-core/nacho/normalise/meta.yml
+++ b/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"

From b7ba0c588ccc6a38debb3945425bff0388f15ce1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 15:22:43 +0000
Subject: [PATCH 09/17] change output

---
 modules/nf-core/nacho/normalise/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
index 495551473ec..e8020924665 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/modules/nf-core/nacho/normalise/main.nf
@@ -12,8 +12,8 @@ process NACHO_NORMALISE {
     tuple val(meta2), path(sample_sheet)
 
     output:
-    path "*normalized_counts.tsv"          , emit: normalized_counts
-    path "*normalized_counts_wo_HKnorm.tsv", emit: normalized_counts_wo_HK
+    path "normalized_counts.tsv"          , emit: normalized_counts
+    path "normalized_counts_wo_HKnorm.tsv", emit: normalized_counts_wo_HK
     path "versions.yml"                    , emit: versions
 
     when:

From b577694fcfdd8b934b40c14b29ea3a1af36d28e2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 16:09:58 +0000
Subject: [PATCH 10/17] add meta to output channels

---
 modules/nf-core/nacho/normalise/main.nf  |  6 +--
 modules/nf-core/nacho/normalise/meta.yml | 51 +++++++++++++++++-------
 2 files changed, 39 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalise/main.nf
index e8020924665..01826d31ebe 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/modules/nf-core/nacho/normalise/main.nf
@@ -12,9 +12,9 @@ process NACHO_NORMALISE {
     tuple val(meta2), path(sample_sheet)
 
     output:
-    path "normalized_counts.tsv"          , emit: normalized_counts
-    path "normalized_counts_wo_HKnorm.tsv", emit: normalized_counts_wo_HK
-    path "versions.yml"                    , emit: versions
+    tuple val(meta), path("normalized_counts.tsv")          , emit: normalized_counts
+    tuple val(meta), path("normalized_counts_wo_HKnorm.tsv"), emit: normalized_counts_wo_HK
+    path "versions.yml"                                     , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/nacho/normalise/meta.yml b/modules/nf-core/nacho/normalise/meta.yml
index 2eccbeaf3eb..b51bc693065 100644
--- a/modules/nf-core/nacho/normalise/meta.yml
+++ b/modules/nf-core/nacho/normalise/meta.yml
@@ -20,36 +20,57 @@ tools:
         For more information `vignette("NACHO")` and `vignette("NACHO-analysis")`
       homepage: https://github.com/mcanouil/NACHO
       documentation: https://cran.r-project.org/web/packages/NACHO/vignettes/NACHO.html
-      doi: "doi:10.1093/bioinformatics/btz647"
+      doi: "10.1093/bioinformatics/btz647"
       licence: [ "GPL-3.0" ]
       identifier: ""
+      args_id: "$args"
 
 input:
-  - - rcc_files:
-      type: file
-      description: |
-        List of RCC files for all samples, which are direct outputs from NanoString runs
-      pattern: "*.RCC"
-  - - sample_sheet:
-      type: "file"
-      pattern: "*.csv"
-      description: |
-        Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - rcc_files:
+        type: file
+        description: |
+          List of RCC files for all samples, which are direct outputs from NanoString runs
+        pattern: "*.RCC"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing file information
+          e.g. [ id:'test_samplesheet' ]
+    - sample_sheet:
+        type: "file"
+        pattern: "*.csv"
+        description: |
+          Comma-separated file with 3 columns: RCC_FILE, RCC_FILE_NAME, and SAMPLE_ID
 
 output:
   - normalized_counts:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
     - "normalized_counts.tsv":
         type: file
         description: |
           Tab-separated file with gene normalized counts for the samples
-        pattern: "*normalized_counts.tsv"
+        pattern: "normalized_counts.tsv"
 
   - normalized_counts_wo_HK:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
     - "normalized_counts_wo_HKnorm.tsv":
         type: file
         description: |
           Tab-separated file with gene normalized counts for the samples, without housekeeping genes.
-        pattern: "*normalized_counts_wo_HKnorm.tsv"
+        pattern: "normalized_counts_wo_HKnorm.tsv"
   - versions:
     - "versions.yml":
         type: file
@@ -58,6 +79,6 @@ output:
         pattern: "versions.yml"
 
 authors:
-  - "@alanmobbs93"
+  - "@alanmmobbs93"
 maintainers:
-  - "@alanmobbs93"
+  - "@alanmmobbs93"

From a3dd7fce8c1884535cc32efe7fe2283f28ab318b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 16:10:12 +0000
Subject: [PATCH 11/17] fix environment.yml linting

---
 modules/nf-core/nacho/normalise/environment.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/environment.yml b/modules/nf-core/nacho/normalise/environment.yml
index a06ce44af9c..9cf652c88fe 100644
--- a/modules/nf-core/nacho/normalise/environment.yml
+++ b/modules/nf-core/nacho/normalise/environment.yml
@@ -1,11 +1,12 @@
----
 channels:
   - conda-forge
+  - bioconda
+
 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-optparse=1.7.5
   - conda-forge::r-readr=2.1.5
   - conda-forge::r-tidyr=1.3.0
-  - conda-forge::r-optparse=1.7.5

From 8fea3b77513bf41cf59c539639bd24d62a6b7332 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 16:33:43 +0000
Subject: [PATCH 12/17] update snaps

---
 .../nacho/normalise/tests/main.nf.test.snap   | 60 +++++++++++++++----
 1 file changed, 50 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
index 6d242b1e833..2a8dfe1be0e 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
@@ -3,19 +3,39 @@
         "content": [
             {
                 "0": [
-                    "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "1": [
-                    "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "2": [
                     "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
                 ],
                 "normalized_counts": [
-                    "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "normalized_counts_wo_HK": [
-                    "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
                 ],
                 "versions": [
                     "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
@@ -26,25 +46,45 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T15:13:12.044326701"
+        "timestamp": "2024-11-27T16:33:31.221669303"
     },
     "Salmon - RCC files": {
         "content": [
             {
                 "0": [
-                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                    ]
                 ],
                 "1": [
-                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                    ]
                 ],
                 "2": [
                     "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
                 ],
                 "normalized_counts": [
-                    "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                    ]
                 ],
                 "normalized_counts_wo_HK": [
-                    "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                    ]
                 ],
                 "versions": [
                     "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
@@ -55,6 +95,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T15:12:49.870804363"
+        "timestamp": "2024-11-27T16:33:11.86337987"
     }
 }
\ No newline at end of file

From 01828c2fb844393a1c57ce888be260d6418fe6df Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Wed, 27 Nov 2024 19:34:45 +0000
Subject: [PATCH 13/17] replace Stub with stub to pass linting

---
 .../nacho/normalise/tests/main.nf.test        |  2 +-
 .../nacho/normalise/tests/main.nf.test.snap   | 24 +++++++++----------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalise/tests/main.nf.test
index d14b0873006..3726ae6195a 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test
@@ -46,7 +46,7 @@ nextflow_process {
         }
     }
 
-    test("Salmon - RCC files - Stub") {
+    test("Salmon - RCC files - stub") {
 
         options "-stub"
         when {
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
index 2a8dfe1be0e..4d7ceb00dbb 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "Salmon - RCC files - Stub": {
+    "Salmon - RCC files": {
         "content": [
             {
                 "0": [
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
                     ]
                 ],
                 "1": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                     ]
                 ],
                 "2": [
@@ -26,7 +26,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
                     ]
                 ],
                 "normalized_counts_wo_HK": [
@@ -34,7 +34,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
                     ]
                 ],
                 "versions": [
@@ -46,9 +46,9 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T16:33:31.221669303"
+        "timestamp": "2024-11-27T19:32:45.057875179"
     },
-    "Salmon - RCC files": {
+    "Salmon - RCC files - stub": {
         "content": [
             {
                 "0": [
@@ -56,7 +56,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -64,7 +64,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -75,7 +75,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts.tsv:md5,a0124c7a24bd04296f441d9ade82a05f"
+                        "normalized_counts.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "normalized_counts_wo_HK": [
@@ -83,7 +83,7 @@
                         {
                             "id": "test"
                         },
-                        "normalized_counts_wo_HKnorm.tsv:md5,5a2ce112c24e1b0d0f4cf3392111ef9e"
+                        "normalized_counts_wo_HKnorm.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
@@ -95,6 +95,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T16:33:11.86337987"
+        "timestamp": "2024-11-27T19:33:06.874199328"
     }
 }
\ No newline at end of file

From 380c3b068ae517aa61926ae225888cc87280744a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?=
 <64787947+alanmmobbs93@users.noreply.github.com>
Date: Wed, 27 Nov 2024 19:35:30 -0300
Subject: [PATCH 14/17] Update main.nf.test

---
 modules/nf-core/nacho/normalise/tests/main.nf.test | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalise/tests/main.nf.test
index 3726ae6195a..642c39bd026 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test
+++ b/modules/nf-core/nacho/normalise/tests/main.nf.test
@@ -22,7 +22,7 @@ nextflow_process {
                 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
+                        .map { row -> return file(row.RCC_FILE, checkIfExists: true) } // Select first column: path to file
                         .collect()
                         .map{ files ->
                             tuple( [id: 'test'], files ) // Add meta component
@@ -83,4 +83,4 @@ nextflow_process {
         }
     }
 
-}
\ No newline at end of file
+}

From f195ac78d173f53f8b913b3b3c8f17b74ecdcb94 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Thu, 28 Nov 2024 15:50:38 +0000
Subject: [PATCH 15/17] change normalise by normalize

---
 .../nf-core/nacho/{normalise => normalize}/environment.yml  | 0
 modules/nf-core/nacho/{normalise => normalize}/main.nf      | 2 +-
 modules/nf-core/nacho/{normalise => normalize}/meta.yml     | 2 +-
 .../{normalise => normalize}/resources/usr/bin/nacho_norm.R | 0
 .../nacho/{normalise => normalize}/tests/main.nf.test       | 6 +++---
 .../nacho/{normalise => normalize}/tests/main.nf.test.snap  | 0
 .../nacho/{normalise => normalize}/tests/nextflow.config    | 0
 7 files changed, 5 insertions(+), 5 deletions(-)
 rename modules/nf-core/nacho/{normalise => normalize}/environment.yml (100%)
 rename modules/nf-core/nacho/{normalise => normalize}/main.nf (99%)
 rename modules/nf-core/nacho/{normalise => normalize}/meta.yml (99%)
 rename modules/nf-core/nacho/{normalise => normalize}/resources/usr/bin/nacho_norm.R (100%)
 rename modules/nf-core/nacho/{normalise => normalize}/tests/main.nf.test (96%)
 rename modules/nf-core/nacho/{normalise => normalize}/tests/main.nf.test.snap (100%)
 rename modules/nf-core/nacho/{normalise => normalize}/tests/nextflow.config (100%)

diff --git a/modules/nf-core/nacho/normalise/environment.yml b/modules/nf-core/nacho/normalize/environment.yml
similarity index 100%
rename from modules/nf-core/nacho/normalise/environment.yml
rename to modules/nf-core/nacho/normalize/environment.yml
diff --git a/modules/nf-core/nacho/normalise/main.nf b/modules/nf-core/nacho/normalize/main.nf
similarity index 99%
rename from modules/nf-core/nacho/normalise/main.nf
rename to modules/nf-core/nacho/normalize/main.nf
index 01826d31ebe..2166639738e 100644
--- a/modules/nf-core/nacho/normalise/main.nf
+++ b/modules/nf-core/nacho/normalize/main.nf
@@ -1,6 +1,6 @@
 nextflow.enable.moduleBinaries = true
 
-process NACHO_NORMALISE {
+process NACHO_NORMALIZE {
     tag "${meta.id}"
     label 'process_single'
 
diff --git a/modules/nf-core/nacho/normalise/meta.yml b/modules/nf-core/nacho/normalize/meta.yml
similarity index 99%
rename from modules/nf-core/nacho/normalise/meta.yml
rename to modules/nf-core/nacho/normalize/meta.yml
index b51bc693065..8fddb762e3a 100644
--- a/modules/nf-core/nacho/normalise/meta.yml
+++ b/modules/nf-core/nacho/normalize/meta.yml
@@ -1,5 +1,5 @@
 ---
-name: nacho_normalise
+name: nacho_normalize
 description: |
   NACHO (NAnostring quality Control dasHbOard) is developed for NanoString nCounter data.
   NanoString nCounter data is a messenger-RNA/micro-RNA (mRNA/miRNA) expression assay and works with fluorescent barcodes.
diff --git a/modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R b/modules/nf-core/nacho/normalize/resources/usr/bin/nacho_norm.R
similarity index 100%
rename from modules/nf-core/nacho/normalise/resources/usr/bin/nacho_norm.R
rename to modules/nf-core/nacho/normalize/resources/usr/bin/nacho_norm.R
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test b/modules/nf-core/nacho/normalize/tests/main.nf.test
similarity index 96%
rename from modules/nf-core/nacho/normalise/tests/main.nf.test
rename to modules/nf-core/nacho/normalize/tests/main.nf.test
index 642c39bd026..ec21ec5c87f 100644
--- a/modules/nf-core/nacho/normalise/tests/main.nf.test
+++ b/modules/nf-core/nacho/normalize/tests/main.nf.test
@@ -1,14 +1,14 @@
 nextflow_process {
 
-    name "Test Process NACHO_NORMALISE"
+    name "Test Process NACHO_NORMALIZE"
     script "../main.nf"
-    process "NACHO_NORMALISE"
+    process "NACHO_NORMALIZE"
     config "./nextflow.config"
 
     tag "modules"
     tag "modules_nfcore"
     tag "nacho"
-    tag "nacho/normalise"
+    tag "nacho/normalize"
 
     test("Salmon - RCC files") {
 
diff --git a/modules/nf-core/nacho/normalise/tests/main.nf.test.snap b/modules/nf-core/nacho/normalize/tests/main.nf.test.snap
similarity index 100%
rename from modules/nf-core/nacho/normalise/tests/main.nf.test.snap
rename to modules/nf-core/nacho/normalize/tests/main.nf.test.snap
diff --git a/modules/nf-core/nacho/normalise/tests/nextflow.config b/modules/nf-core/nacho/normalize/tests/nextflow.config
similarity index 100%
rename from modules/nf-core/nacho/normalise/tests/nextflow.config
rename to modules/nf-core/nacho/normalize/tests/nextflow.config

From e4e779b61ddd9a8f8cb466b7dc13e1b97b4a6919 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Thu, 28 Nov 2024 18:03:10 +0000
Subject: [PATCH 16/17] move moduleBinaries to test nextflow config

---
 modules/nf-core/nacho/normalize/main.nf               | 2 --
 modules/nf-core/nacho/normalize/tests/nextflow.config | 2 ++
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/nacho/normalize/main.nf b/modules/nf-core/nacho/normalize/main.nf
index 2166639738e..69cc49ec143 100644
--- a/modules/nf-core/nacho/normalize/main.nf
+++ b/modules/nf-core/nacho/normalize/main.nf
@@ -1,5 +1,3 @@
-nextflow.enable.moduleBinaries = true
-
 process NACHO_NORMALIZE {
     tag "${meta.id}"
     label 'process_single'
diff --git a/modules/nf-core/nacho/normalize/tests/nextflow.config b/modules/nf-core/nacho/normalize/tests/nextflow.config
index 918ae6f89ed..e64446a7c4d 100644
--- a/modules/nf-core/nacho/normalize/tests/nextflow.config
+++ b/modules/nf-core/nacho/normalize/tests/nextflow.config
@@ -1,3 +1,5 @@
+nextflow.enable.moduleBinaries = true
+
 process {
     withName: 'NACHO_NORMALISE' {
         ext.args = params.module_args

From aa2faad335385a6a18964a95d85f6edd36d38414 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Alan=20M=C3=B6bbs?= <alanmmobbs@gmail.com>
Date: Thu, 28 Nov 2024 18:32:32 +0000
Subject: [PATCH 17/17] update snapshot after renaming

---
 .../nf-core/nacho/normalize/tests/main.nf.test.snap  | 12 ++++++------
 .../nf-core/nacho/normalize/tests/nextflow.config    |  2 +-
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/nacho/normalize/tests/main.nf.test.snap b/modules/nf-core/nacho/normalize/tests/main.nf.test.snap
index 4d7ceb00dbb..f6e20e3947d 100644
--- a/modules/nf-core/nacho/normalize/tests/main.nf.test.snap
+++ b/modules/nf-core/nacho/normalize/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                    "versions.yml:md5,dbc82908e1d1fcd2429022a4f327b9ba"
                 ],
                 "normalized_counts": [
                     [
@@ -38,7 +38,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                    "versions.yml:md5,dbc82908e1d1fcd2429022a4f327b9ba"
                 ]
             }
         ],
@@ -46,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T19:32:45.057875179"
+        "timestamp": "2024-11-28T18:31:49.03241566"
     },
     "Salmon - RCC files - stub": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                    "versions.yml:md5,dbc82908e1d1fcd2429022a4f327b9ba"
                 ],
                 "normalized_counts": [
                     [
@@ -87,7 +87,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,a67e277a3788bf01023f086295e6fab1"
+                    "versions.yml:md5,dbc82908e1d1fcd2429022a4f327b9ba"
                 ]
             }
         ],
@@ -95,6 +95,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-11-27T19:33:06.874199328"
+        "timestamp": "2024-11-28T18:32:02.81614763"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/nacho/normalize/tests/nextflow.config b/modules/nf-core/nacho/normalize/tests/nextflow.config
index e64446a7c4d..b08db067be7 100644
--- a/modules/nf-core/nacho/normalize/tests/nextflow.config
+++ b/modules/nf-core/nacho/normalize/tests/nextflow.config
@@ -1,7 +1,7 @@
 nextflow.enable.moduleBinaries = true
 
 process {
-    withName: 'NACHO_NORMALISE' {
+    withName: 'NACHO_NORMALIZE' {
         ext.args = params.module_args
     }
 }