From c46fd8606fa32812004220b4a7a62dd98b72260d Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Mon, 31 Jul 2023 10:34:53 +0200 Subject: [PATCH] update readme [ci skip] --- README.md | 23 +++++++---------------- 1 file changed, 7 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 7aedf04..d53725c 100644 --- a/README.md +++ b/README.md @@ -15,39 +15,30 @@ nextflow run https://github.com/nf-modules-hub/tb-profiler ## Options - -- `collate` - -For collating the individual results obtained by running `tb-profiler` you can set pass this option. - -``` -nextflow run https://github.com/nf-modules-hub/tb-profiler --collate -``` - -- `filePattern` +- `file_pattern` By default, the process assumes the files to follow the `*_{R1,R2}.fastq.gz` pattern, which could be customized using this option ``` -nextflow run https://github.com/nf-modules-hub/tb-profiler --filePattern './*_{1,2}.fastq.gz' +nextflow run https://github.com/nf-modules-hub/tb-profiler --file_pattern './*_{1,2}.fastq.gz' ``` -- `resultsDir` +- `outdir` By default, it stores the result files locally inside the `results` directory. ``` -nextflow run https://github.com/nf-modules-hub/tb-profiler --resultsDir /path/to/custom/resultsDir +nextflow run https://github.com/nf-modules-hub/tb-profiler --outdir /path/to/custom/resultsDir ``` -- `saveMode` +- `publish_dir_mode` -By default, the pipeline publishes the results in the `resultsDir` by copying the relevant output. +By default, the pipeline publishes the results in the `outdir` by copying the relevant output. You can update this behavior by simply specifying the alternative such as `move` or `link` etc. ``` -nextflow run https://github.com/nf-modules-hub/tb-profiler --saveMode move +nextflow run https://github.com/nf-modules-hub/tb-profiler --publish_dir_mode move ``` For more information please refer [Nextflow documentation](https://www.nextflow.io/docs/latest/process.html#publishdir)