From 54ee65ba4cb04c02885b0918fa01619b638281a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?S=C3=A9bastien=20Guizard?= Date: Mon, 19 Feb 2024 11:15:50 +0000 Subject: [PATCH] Add language to code blocks and add full example command --- README.md | 48 +++++++++++++++++++++++++++++++----------------- 1 file changed, 31 insertions(+), 17 deletions(-) diff --git a/README.md b/README.md index 159b02c..5937b5d 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ The only dependencies are: My advice for installation is to use [conda (Miniforge)](https://github.com/conda-forge/miniforge) package manager. -``` +```bash conda create -n nf-mixcr_env conda activate nf-mixcr_env conda install -c milaboratories nextflow singularity mixcr @@ -61,13 +61,13 @@ The test profile can be use to run to the pipeline with toy datasets automatical You can start the test by running: -``` +```bash nextflow run sguizard/nf-mixcr -profile singularity,test, ``` or if you use docker in place of singularity: -``` +```bash nextflow run sguizard/nf-mixcr -profile docker,test, ``` @@ -79,7 +79,7 @@ The place holder must be replaced by your cluster profile. The lis To keep files sorted between inputs, outputs and working directories, I start by creating a directory for the analysis (TCR_project) and create a data directory where I store the reads and other inputs files: -``` +```txt TCR_project/ └── data ├── imgt.202312-3.sv8.json.gz @@ -93,7 +93,7 @@ TCR_project/ A sampleesheet must be provided. This file is a three columns comma-separated value table. The columns are `id`, `read1`, `read2` and each value must be separated by a comma. Each line gives the location of the fastq file associated with a unique ID. -``` +```csv id,read1,read2 SAMP1,./data/read_1.fastq.gz,./data/read_2.fastq.gz ``` @@ -108,7 +108,7 @@ MiXCR gather multiple tools and each of them are highly configurable. Implementi Each line between the central square brackets is a `mixcr analyze` option. If needed, you can add options by inserting a new line at the end of the option, write your option between **simple quotes** and ending the line with a **comma**. -``` +```txt process { withName: MIXCR_ANALYZE { cpus = 8 @@ -130,7 +130,7 @@ process { The classical command line to run the pipeline looks like this: -``` +```bash nextflow run sguizard/nf-mixcr \ -profile \ -c data/mixcr_analyze.config \ @@ -172,7 +172,7 @@ The **compulsory** options are: The results of the pipeline will be stored in the directory defined by the `--outdir` option. For each process/program, one directory will be created to store the results. An additional directory, `pipeline_info`, gather reports about pipeline execution. -``` +```txt / |-- 01_mixcr_analysis |-- 02_mixcr_exportClones @@ -185,7 +185,7 @@ The results of the pipeline will be stored in the directory defined by the `--ou ### 01_mixcr_analysis -``` +```txt 01_mixcr_analysis |-- SAMP1.align.report.json |-- SAMP1.align.report.txt @@ -206,7 +206,7 @@ This directory gather the results of the programs launched by MiXCR. With the pr ### 02_mixcr_exportClones -``` +```txt 02_mixcr_exportClones `-- SAMP1_exportClones_.tsv ``` @@ -215,7 +215,7 @@ This directory gather the results of the programs launched by MiXCR. With the pr ### 03_mixcr_exportQc_align -``` +```txt 03_mixcr_exportQc_align |-- TCR_exportQC_align.pdf `-- TCR_exportQC_align.png @@ -226,7 +226,7 @@ It describes the reads status (correctly/incorrectly align). ### 03_mixcr_exportQc_chainusage -``` +```txt 03_mixcr_exportQc_chainusage |-- TCR_exportQC_chainUsage.pdf `-- TCR_exportQC_chainUsage.png @@ -236,7 +236,7 @@ Exports chain usage summary of each sample. ### 03_mixcr_exportQc_coverage -``` +```txt 03_mixcr_exportQc_coverage |-- SAMP1_exportQC_coverage.pdf |-- SAMP1_exportQC_coverage_R0.png @@ -248,7 +248,7 @@ Exports anchor points coverage by the library. It separately plots coverage for ### 04_mixcr_exportReports -``` +```txt 04_mixcr_exportReports |-- SAMP1.report.json `-- SAMP1.report.txt @@ -258,7 +258,7 @@ These files contains the report of each tool launched by `mixcr analyze`. ### pipeline_info -``` +```txt pipeline_info |-- _execution_report.html |-- _execution_timeline.html @@ -284,7 +284,7 @@ This error is caused by the permission of the `/exports/igmm/eddie/Bioinformatic In order to fix this, you can create an `eddie_fix.confg` file and add the following lines to it: -``` +```txt singularity { envWhitelist = "SINGULARITY_TMPDIR,TMPDIR" runOptions = '-p -B "$TMPDIR"' @@ -305,7 +305,7 @@ This is obviously a temporary fix. Discussions are running at the Roslin Institu To being sure that MiXCR can correctly access to your license, you should update the singularity `-B` option by adding this following lines into a custom configuration file (eddie_fix.config for example 😜). -``` +```txt singularity { runOptions = '-p -B "$TMPDIR",/home/' } @@ -313,6 +313,20 @@ singularity { Do not forget to replace the placeholder with yours. + +### Example command line + +```bash +nextflow run sguizard/nf-mixcr \ + -profile eddie \ + -c data/mixcr_analyze.config \ + -c data/eddie_fix.config \ + --samplesheet data/samplesheet.csv \ + --preset generic-amplicon-with-umi \ + --library data/imgt.202312-3.sv8.json.gz \ + --study TCR_cat_project +``` + ## Contributing Contributions are welcome! Just try to following the code formatting the best as you can.