Merge branch 'dev' into nf-core-template-merge-2.14.1

Author: mashehu

.github/workflows/ci.yml

@@ -39,8 +39,5 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results

CITATIONS.md

@@ -14,6 +14,10 @@
 
   > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
+- [fastp](https://www.ncbi.nlm.nih.gov/pubmed/30423086/)
+
+  > Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018 Sep 1;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560. PubMed PMID: 30423086; PubMed Central PMCID: PMC6129281.
+
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

README.md

@@ -19,46 +19,35 @@
 
 ## Introduction
 
-**nf-core/demo** is a bioinformatics pipeline that ...
+**nf-core/demo** is a simple nf-core style bioinformatics pipeline for workshops and demonstrations. It was created using the nf-core template and is designed to run quickly using small test data files.
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+![nf-core/demo metro map](docs/images/nf-core-demo-subway.png)
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+1. Read QC ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
+2. Adapter and quality trimming ([`FASTP`](https://github.com/OpenGene/fastp))
+3. Present QC for raw reads ([`MULTIQC`](http://multiqc.info/))
 
 ## Usage
 
 > [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
 sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+SAMPLE1_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
+SAMPLE2_PE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
+SAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,
+SAMPLE3_SE,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,
 ```
 
 Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
 
--->
-
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/demo \
    -profile <docker/singularity/.../institute> \
@@ -80,11 +69,9 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/demo was originally written by Christopher Hakkaart.
-
-We thank the following people for their extensive assistance in the development of this pipeline:
+nf-core/demo was originally written by Chris Hakkaart ([@christopher-hakkaart](https://github.com/christopher-hakkaart)).
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+<!-- We thank the following people for their extensive assistance in the development of this pipeline: -->
 
 ## Contributions and Support
 
@@ -97,8 +84,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use nf-core/demo for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/demo Methods Description"
 section_href: "https://github.com/nf-core/demo"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { check_max( 1    * task.attempt, 'cpus'   ) }
     memory = { check_max( 6.GB * task.attempt, 'memory' ) }
     time   = { check_max( 4.h  * task.attempt, 'time'   ) }
@@ -20,12 +19,6 @@ process {
     maxErrors     = '-1'
 
     // Process-specific resource requirements
-    // NOTE - Please try and re-use the labels below as much as possible.
-    //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
-    //        If possible, it would be nice to keep the same label naming convention when
-    //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
-    // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }
         memory = { check_max( 6.GB * task.attempt, 'memory'  ) }

conf/modules.config

@@ -20,6 +20,20 @@ process {
 
     withName: FASTQC {
         ext.args = '--quiet'
+        publishDir = [
+            path: { "${params.outdir}/fastqc/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.{html,json}"
+        ]
+    }
+
+
+    withName: 'FASTP' {
+        publishDir = [
+            path: { "${params.outdir}/fastp/${meta.id}" },
+            mode: params.publish_dir_mode,
+            pattern: "*.{html,json,log}"
+        ]
     }
 
     withName: 'MULTIQC' {

conf/test.config

@@ -20,8 +20,6 @@ params {
     max_time   = '6.h'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
 
     // Genome references

conf/test_full.config

@@ -15,8 +15,6 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
     input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
 
     // Genome references