New Module: NACHO_QC (#7108)

* initialize module

* update test

* Remove TO-DO from main.nf.test

* Remove comment from main.nf.test

* update test after meta component in output channels

* split channel into png and txt outputs

* update meta file

* move moduleBinaries to test nextflow config

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

@@ -0,0 +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

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

@@ -0,0 +1,77 @@
+process NACHO_QC {
+    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:
+    tuple val(meta) , path(rcc_files, stageAs: "input/*")
+    tuple val(meta2), path(sample_sheet)
+
+    output:
+    tuple val(meta), path("*.html")   , emit: nacho_qc_reports
+    tuple val(meta), path("*_mqc.png"), emit: nacho_qc_png
+    tuple val(meta), path("*_mqc.txt"), emit: nacho_qc_txt
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    nacho_qc.R \\
+        --input_rcc_path input \\
+        --input_samplesheet ${sample_sheet}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${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')))")
+        r-optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch qc.html
+    touch qc_with_outliers.html
+    touch AVG_vs_BD_mqc.png
+    touch AVG_vs_MED_mqc.png
+    touch BD_mqc.png
+    touch FOV_mqc.png
+    touch HKF_mqc.png
+    touch HK_mqc.png
+    touch LOD_mqc.png
+    touch Neg_mqc.png
+    touch PCA1_vs_PCA2_mqc.png
+    touch PCAi_mqc.png
+    touch PCA_mqc.png
+    touch plot_normf_mqc.png
+    touch Posctrl_linearity_mqc.png
+    touch POSF_vs_NEGF_mqc.png
+    touch Pos_mqc.png
+    touch Pos_vs_neg_mqc.png
+    touch normalized_qc_mqc.txt
+    touch hk_detected_mqc.txt
+
+    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')))")
+        r-optparse: \$(Rscript -e "library(optparse); cat(as.character(packageVersion('optparse')))")
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,89 @@
+name: nacho_qc
+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:
+  - nacho
+  - nanostring
+  - mRNA
+  - miRNA
+  - qc
+tools:
+  - 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: "10.1093/bioinformatics/btz647"
+      licence: [ "GPL-3.0" ]
+      identifier: ""
+input:
+  - - 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:
+  - nacho_qc_reports:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - "*.html":
+        type: file
+        description: |
+          HTML report
+        pattern: "*.html"
+  - nacho_qc_png:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - "*_mqc.png":
+        type: file
+        description: |
+          Output PNG files
+        pattern: "*_mqc.png"
+  - nacho_qc_txt:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - "*_mqc.txt":
+        type: file
+        description: |
+          Plain text reports
+        pattern: "*_mqc.txt"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: |
+          File containing software versions
+        pattern: "versions.yml"
+authors:
+  - "@alanmmobbs93"
+maintainers:
+  - "@alanmmobbs93"