From 56608c0ad44aaded8ea1c2bf2a70da3204e012b8 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Fri, 26 Jul 2019 16:05:13 +0100 Subject: [PATCH] FastQC prototype with docs --- README.md | 6 ++---- docs/fastqc.md | 2 -- docs/template.md | 2 -- nf/fastqc.nf | 34 +++++++++++++++++++++++++++++++++- 4 files changed, 35 insertions(+), 9 deletions(-) delete mode 100644 docs/fastqc.md delete mode 100644 docs/template.md diff --git a/README.md b/README.md index fea0f299..acea84a7 100644 --- a/README.md +++ b/README.md @@ -55,13 +55,11 @@ If you want to add a new module config file to `nf-core/modules` please test tha ### Documentation -You will have to create a [Markdown document](https://www.markdownguide.org/getting-started/) outlining the details required to use the module file and extensive links to documentation for the tool(s) used in the module file. You can use the provided [`docs/template.md`](docs/template.md) to guide you as to how to do this appropriately. - -See [`nf-core/modules/docs`](https://github.com/nf-core/modules/tree/master/docs) for examples. +Please add some documentation to the top of the module file in the form of native Nextflow comments. This has to be specified in a particular format as you will be able to see from other examples in the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory. ### Uploading to `nf-core/modules` -[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory, and the documentation file to the [`nf-core/modules/docs`](https://github.com/nf-core/modules/tree/master/docs) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively. +[Fork](https://help.github.com/articles/fork-a-repo/) the `nf-core/modules` repository to your own GitHub account. Within the local clone of your fork add the module file to the [`nf-core/modules/nf`](https://github.com/nf-core/modules/tree/master/nf) directory. Please keep the naming consistent between the module and documentation files e.g. `bwa.nf` and `bwa.md`, respectively. Commit and push these changes to your local clone on GitHub, and then [create a pull request](https://help.github.com/articles/creating-a-pull-request-from-a-fork/) on `nf-core/modules` GitHub repo with the appropriate information. diff --git a/docs/fastqc.md b/docs/fastqc.md deleted file mode 100644 index d714627e..00000000 --- a/docs/fastqc.md +++ /dev/null @@ -1,2 +0,0 @@ - -# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON! diff --git a/docs/template.md b/docs/template.md deleted file mode 100644 index d714627e..00000000 --- a/docs/template.md +++ /dev/null @@ -1,2 +0,0 @@ - -# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON! diff --git a/nf/fastqc.nf b/nf/fastqc.nf index d714627e..a5e8bd7f 100644 --- a/nf/fastqc.nf +++ b/nf/fastqc.nf @@ -1,2 +1,34 @@ +/* +* Description: +* Run FastQC on sequenced reads +* Keywords: +* read qc +* adapter +* Tools: +* FastQC: +* homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ +* documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ +* 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. +*/ +process fastqc { + tag "$sample_id" + publishDir "${params.outdir}/fastqc", mode: 'copy', + saveAs: {filename -> filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename"} -# COMING TO A NEXTFLOW PIPELINE NEAR YOU SOON! + input: + set val(sample_id), file(reads) + + output: + file "*_fastqc.{zip,html}" + + script: + """ + fastqc -q $reads + + fastqc --version &> fastqc.version.txt + """ +}