From 38c7542a94c375aa2f6202ffa658e992e55892fa Mon Sep 17 00:00:00 2001 From: ggabernet Date: Fri, 27 Mar 2020 17:47:15 +0100 Subject: [PATCH 1/3] markdup_java_options docs --- CHANGELOG.md | 1 + docs/usage.md | 9 +++++++++ 2 files changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e3139fc58d..928005698a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a - [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` version `3.3.0` - [#163](https://github.com/nf-core/sarek/pull/163) - Add [MSIsensor](https://github.com/ding-lab/msisensor) in tools and container - [#164](https://github.com/nf-core/sarek/pull/164) - Add `--no_gatk_spark` params and tests +- [#166](https://github.com/nf-core/sarek/issues/166) - Add `--markdup_java_options` documentation ### Changed diff --git a/docs/usage.md b/docs/usage.md index 6087b803f1..41844109ae 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -79,6 +79,7 @@ - [Job resources](#job-resources) - [Automatic resubmission](#automatic-resubmission) - [Custom resource requests](#custom-resource-requests) + - [--markdup_java_options](#--markdup_java_options) - [AWSBatch specific parameters](#awsbatch-specific-parameters) - [--awsqueue](#--awsqueue) - [--awsregion](#--awsregion) @@ -777,6 +778,14 @@ You can then create a pull request to the `nf-core/configs` repository with the If you have any questions or issues please send us a message on [Slack](https://nf-co.re/join/slack). +## --markdup_java_options + +To control the java options necessary for the GATK `MarkDuplicates` process, you can set this parameter. For example (those are the default settings): + +```bash +--markdup_java_options "-Xms4000m -Xmx7g" +``` + ## AWSBatch specific parameters Running the pipeline on AWSBatch requires a couple of specific parameters to be set according to your AWSBatch configuration. From 674e1566e2eb40448ec6d519589390c7c50ac1cf Mon Sep 17 00:00:00 2001 From: ggabernet Date: Sun, 29 Mar 2020 16:49:09 +0200 Subject: [PATCH 2/3] update to params input in docs --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 41844109ae..ceaf852d8d 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,7 +6,7 @@ - [Reproducibility](#reproducibility) - [Main arguments](#main-arguments) - [-profile](#-profile) - - [`--reads`](#--reads) + - [`--input`](#--input) - [--split_fastq](#--split_fastq) - [--trim_fastq](#--trim_fastq) - [--clip_r1](#--clip_r1) @@ -197,7 +197,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A profile with a complete configuration for automated testing - Includes links to test data so needs no other parameters -### `--reads` +### `--input` Use this to specify the location of your input FastQ files. For example: From bef4e1876d4aa1391025a10a546db0f8cee2fb2e Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Mon, 30 Mar 2020 10:29:03 +0200 Subject: [PATCH 3/3] Apply suggestions from code review --- docs/usage.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index ceaf852d8d..0ce5d66af0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,7 +6,7 @@ - [Reproducibility](#reproducibility) - [Main arguments](#main-arguments) - [-profile](#-profile) - - [`--input`](#--input) + - [--input](#--input) - [--split_fastq](#--split_fastq) - [--trim_fastq](#--trim_fastq) - [--clip_r1](#--clip_r1) @@ -197,7 +197,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - A profile with a complete configuration for automated testing - Includes links to test data so needs no other parameters -### `--input` +### --input Use this to specify the location of your input FastQ files. For example: