Merge pull request #59 from drpatelh/master

Refine module TEMPLATE

README.md

@@ -11,6 +11,7 @@ A repository for hosting [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl
 
 - [Using existing modules](#using-existing-modules)
 - [Adding a new module file](#adding-a-new-module-file)
+    - [Module template](#module-template)
     - [Guidelines](#guidelines)
     - [Testing](#testing)
     - [Documentation](#documentation)
@@ -108,6 +109,25 @@ and to everyone within the Nextflow community! See
 [`software/`](software)
 for examples.
 
+### Module template
+
+We have added a directory called [`software/SOFTWARE/TOOL/`](software/SOFTWARE/TOOL/) that serves as a template with which to create your own module submission. Where applicable, we have added extensive `TODO` statements to the files in this directory for general information, to help guide you as to where to make the appropriate changes, and how to make them. If in doubt, have a look at how we have done things for other modules.
+
+```console
+.
+├── software
+│   ├── SOFTWARE
+│   │   └── TOOL
+│   │       ├── functions.nf          ## Utility functions imported in main module script
+│   │       ├── main.nf               ## Main module script
+│   │       ├── meta.yml              ## Documentation for module, input, output, params, author
+│   │       └── test
+│   │           ├── input             ## Soft-link input test data from "tests/"
+│   │           ├── main.nf           ## Minimal workflow to test module
+│   │           ├── nextflow.config   ## Minimal config to test module
+│   │           └── output            ## Upload output files from test for unit testing
+```
+
 ### Guidelines
 
 The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in [RFC 2119](https://tools.ietf.org/html/rfc2119).
@@ -202,12 +222,14 @@ We also use a standardised parameter called `params.publish_dir_mode` that can b
 
 - Every module MUST be tested by adding a test workflow with a toy dataset in the [`test/`](software/fastqc/test) directory of the module.
 
-- Generic files from [`tests/data/`](tests/data/) SHOULD be reused by symlinking them into the [`test/input/`](software/fastqc/test/input/) directory of the module.
+- Generic files from [`tests/data/`](tests/data/) MUST be reused by symlinking them into the [`test/input/`](software/fastqc/test/input/) directory of the module.
 
-- Any outputs produced by the test workflow SHOULD be placed in a folder called [`test/output/`](software/fastqc/test/output/) so that they can be used for unit testing.
+- Any outputs produced by the test workflow MUST be placed in a folder called [`test/output/`](software/fastqc/test/output/) so that they can be used for unit testing.
 
 - If the appropriate test data doesn't exist for your module then it MUST be added to [`tests/data/`](tests/data/).
 
+- A GitHub Actions workflow file MUST be added to [`.github/workflows/`](.github/workflows/) e.g. [`.github/workflows/fastqc.yml`](.github/workflows/fastqc.yml).
+
 ### Documentation
 
 - A module MUST be documented in the [`meta.yml`](software/fastqc/meta.yml) file. It MUST document `params`, `input` and `output`. `input` and `output` MUST be a nested list.

software/SOFTWARE/TOOL/meta.yml

@@ -1,42 +1,77 @@
-name: bwa mem
-description: Performs fastq alignment to a fasta reference using the burrows-wheeler aligner
+## TODO nf-core: Please delete all of these TODO statements once the file has been curated
+## TODO nf-core: Change the name of "software_tool" below
+name: software_tool
+## TODO nf-core: Add a description and keywords
+description: Run FastQC on sequenced reads
 keywords:
-    - mem
-    - bwa
-    - alignment
+  - Quality Control
+  - QC
+  - Adapters
 tools:
-    - bwa:
-        description: |
-            BWA is a software package for mapping DNA sequences against a large reference genome, such as the human genome.
-        homepage: http://bio-bwa.sourceforge.net/
-        documentation: http://www.htslib.org/doc/samtools.html
-        arxiv: arXiv:1303.3997
+  ## TODO nf-core: Change the name of "software_tool" below
+  - software_tool:
+      ## TODO nf-core: Add a description and other details for the tool below
+      description: |
+        FastQC gives general quality metrics about your reads.
+        It provides information about the quality score distribution
+        across your reads, the per base sequence content (%A/C/G/T).
+        You get information about adapter contamination and other
+        overrepresented sequences.
+      homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+      documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/
+## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below
+params:
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+## TODO nf-core: Add a description of all of the variables used as input
 input:
-    -
-        - id:
-            type: val
-            description: read/read pair id
-        - reads:
-            type: file
-            description: Input fastq file
-            pattern: "*.{fastq,fq}"
-        - index:
-            type: file
-            description: bwa indexes file
-            pattern: "*.{amb,ann,bwt,pac,sa}"
-        - prefix:
-            type: val
-            description: bwa index prefix, equivalent to index file names without extensions. Usually the reference genome file name unless otherwise specified.
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+        respectively.
+  - options:
+      type: map
+      description: |
+        Groovy Map containing module options for passing command-line arguments and
+        output file paths.
+## TODO nf-core: Add a description of all of the variables used as output
 output:
-    -
-        - bam:
-            type: file
-            description: Output bam file
-            pattern: "*.bam"
-        - bamindex:
-            type: file
-            description: Output bam index file
-            pattern: "*.bai"
-
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
+      type: file
+      description: FastQC report
+      pattern: "*_fastqc.html"
+  - zip:
+      type: file
+      description: FastQC report archive
+      pattern: "*_fastqc.zip"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
+## TODO nf-core: Add your GitHub username below
 authors:
-    - "@jeremy1805"
+  - "@your_github_username"

software/SOFTWARE/TOOL/test/main.nf

@@ -2,14 +2,34 @@
 
 nextflow.enable.dsl = 2
 
-include '../../../../tests/functions/check_process_outputs.nf' params(params)
-include '../main.nf' params(params)
+include { FASTQC } from '../main.nf'
 
-reads = '../../../../test-datasets/tools/bwa/mem/reads/*_R{1,2}_001.fastq.gz'
-index = '../../../../test-datasets/tools/bwa/mem/index/H3N2.{amb,ann,bwt,pac,sa}'
-prefix = 'H3N2'
+/*
+ * Test with single-end data
+ */
+workflow test_single_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:true ], // meta map
+              [ file("${baseDir}/input/test_single_end.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC ( input, [ publish_dir:'test_single_end' ] )
+}
+
+/*
+ * Test with paired-end data
+ */
+workflow test_paired_end {
+
+    def input = []
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("${baseDir}/input/test_R1.fastq.gz", checkIfExists: true),
+                file("${baseDir}/input/test_R2.fastq.gz", checkIfExists: true) ] ]
+
+    FASTQC ( input, [ publish_dir:'test_paired_end' ] )
+}
 
 workflow {
-  read_input=Channel.fromFilePairs(reads)
-  bwa_mem(read_input,file(index),prefix)
+    test_single_end()
+    test_paired_end()
 }

software/SOFTWARE/TOOL/test/nextflow.config

@@ -1,2 +1,20 @@
-docker.enabled = true
-params.outdir = './results'
+
+params {
+  outdir = "output/"
+  publish_dir_mode = "copy"
+  conda = false
+}
+
+profiles {
+  conda  {
+    params.conda = true
+  }
+  docker {
+    docker.enabled = true
+    docker.runOptions = '-u \$(id -u):\$(id -g)'
+  }
+  singularity {
+    singularity.enabled = true
+    singularity.autoMounts = true
+  }
+}

software/fastqc/meta.yml

@@ -41,11 +41,29 @@ input:
       description: |
         List of input FastQ files of size 1 and 2 for single-end and paired-end data,
         respectively.
+  - options:
+      type: map
+      description: |
+        Groovy Map containing module options for passing command-line arguments and
+        output file paths.
 output:
-  - report:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - html:
       type: file
       description: FastQC report
-      pattern: "*_fastqc.{zip,html}"
+      pattern: "*_fastqc.html"
+  - zip:
+      type: file
+      description: FastQC report archive
+      pattern: "*_fastqc.zip"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.version.txt"
 authors:
   - "@drpatelh"
   - "@grst"