From 1bd36378f98bd609c02bd5988516855f2f0bb1cd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alexander=20Bender=20=28n=C3=A9=20Toenges=29?= <21218078+ATpoint@users.noreply.github.com> Date: Fri, 28 Jul 2023 09:29:16 +0100 Subject: [PATCH 1/2] note on '--tools' in Quickstart --- docs/usage.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 541219ec4..a5093ac9a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -16,10 +16,11 @@ Sarek is designed to handle single samples, such as single-normal or single-tumo The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/sarek --input samplesheet.csv --outdir --genome GATK.GRCh38 -profile docker +nextflow run nf-core/sarek --input samplesheet.csv --outdir --genome GATK.GRCh38 --tools -profile docker ``` -This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. +This will launch the pipeline and perform variant calling with the tools specified in `--tools`, see the [parameter section](https://nf-co.re/sarek/3.2.3/parameters#tools) for details on variant calling tools. +In the above example the pipeline runs with the `docker` configuration profile. See below for more information about profiles. Note that the pipeline will create the following files in your working directory: From 7175be38b29cd8bbdd3488587cb48dc61c204e99 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 28 Jul 2023 08:42:53 +0000 Subject: [PATCH 2/2] [automated] Fix linting with Prettier --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c963ffbc..362d330cd 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1203,7 +1203,7 @@ Ruotes is one of the main massif in the Sarek National Park. - [#607](https://github.com/SciLifeLab/Sarek/pull/607) - Update to `GATK4` - [#608](https://github.com/SciLifeLab/Sarek/pull/608) - Update `Nextflow` required version - [#616](https://github.com/SciLifeLab/Sarek/pull/616) - Update `CHANGELOG` -- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated ` Nextflow ``$name ` syntax with `withName` +- [#617](https://github.com/SciLifeLab/Sarek/pull/617) - Replace deprecated `Nextflow ``$name` syntax with `withName` ### Fixed