From 635e3cb95de30e98ba9967690cacf1d749fc17fc Mon Sep 17 00:00:00 2001 From: jessicaw9910 Date: Thu, 18 Jul 2024 11:08:26 -0400 Subject: [PATCH] added links to modules in README --- nextflow/README.md | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/nextflow/README.md b/nextflow/README.md index d8d9ade..45b7f00 100644 --- a/nextflow/README.md +++ b/nextflow/README.md @@ -5,13 +5,17 @@ To run the pipeline on Iris use: `nextflow run main.nf -params-file params.json -profile iris` It is recommended that each workflow in `main.nf` is run sequentially to allow for users to inspect intermediate QC results and select optimal parameters for downstream tasks: -- The first workflow runs `fastqc` on the raw fastq files and then `multiqc` on those results + +1. The first workflow runs [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) on the raw fastq files and then [`MultiQC`](http://multiqc.info/) on those results - To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTQC_FASTQ` -- The second workflow runs `fastp` to trim adapters and/or poly-X or poly-A tails, followed by `fastq` and `multiqc` + +2. The second workflow runs [`fastp`](https://github.com/OpenGene/fastp) to trim adapters and/or poly-X or poly-A tails, followed by [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and [`MultiQC`](http://multiqc.info/) - To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry FASTP_FASTQ` -- The third workflow runs `star` on the adapter-trimmed fastq files followed by `samtools` indexing + +3. The third workflow runs [`STAR`](https://github.com/alexdobin/STAR) on the adapter-trimmed fastq files followed by [`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) indexing - To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry STAR_FASTQ` -- The fourth workflow runs QC on the resulting BAM files (`samtools flagstat` and various `rseqc` modules), followed by `multiqc` + +4. The fourth workflow runs QC on the resulting BAM files ([`SAMtools`](https://sourceforge.net/projects/samtools/files/samtools/) `flagstat` and various [`RSeQC`](http://rseqc.sourceforge.net/) modules), followed by [`MultiQC`](http://multiqc.info/) on those results - To run this workflow alone use: `nextflow run main.nf -params-file params.json -profile iris -entry QC_BAM` ## Environment