From 5f89f032d83b8fed714ce5c39fc2fc1e7ffc3e2b Mon Sep 17 00:00:00 2001 From: Sateesh Date: Mon, 16 Dec 2024 11:15:33 +0000 Subject: [PATCH] format suggestions from code review --- docs/output.md | 4 +++- docs/usage.md | 10 ++++++++-- nextflow.config | 2 +- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/docs/output.md b/docs/output.md index 94603fc8..21534c6b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution -### Output Directories +### Example output directories of nf-core/methylseq `-test` profile run #### Bismark @@ -83,6 +83,8 @@ bwameth/ └── logs ``` +### Detailed Output Descriptions + ### FastQC
diff --git a/docs/usage.md b/docs/usage.md index 3000ab96..781d8714 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -155,9 +155,15 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c Additional arguments can be appended to a command in a module by specifying them within the module’s custom configuration. The configurations for modules and subworkflows used in the pipeline can be found in `conf/modules` or `conf/subworkflows`. A module’s publishDir path can also be customized in these configurations. -For example, users working with unfinished genomes containing tens or even hundreds of thousands of scaffolds, contigs, or chromosomes often encounter errors when pre-sorting reads into individual chromosome files. These errors are typically caused by the operating system’s limit on the number of file handles that can be open simultaneously (usually 1024; to find out this limit on Linux, use the command: ulimit -a). +For example, users working with unfinished genomes containing tens or even hundreds of thousands of scaffolds, contigs, or chromosomes often encounter errors when pre-sorting reads into individual chromosome files. -To bypass this limitation, the `--scaffolds` option can be added as an additional `ext.args` in `conf/modules/bismark_methylationextractor.config`. This prevents methylation calls from being pre-sorted into individual chromosome files. Instead, all input files are temporarily merged into a single file (unless there is only one file), which is then sorted by both chromosome and position using the Unix sort command. +These errors are typically caused by the operating system’s limit on the number of file handles that can be open simultaneously (usually 1024; to find out this limit on Linux, use the command: ulimit -a). + +To bypass this limitation, the `--scaffolds` option can be added as an additional `ext.args` in `conf/modules/bismark_methylationextractor.config`. + +This prevents methylation calls from being pre-sorted into individual chromosome files. + +Instead, all input files are temporarily merged into a single file (unless there is only one file), which is then sorted by both chromosome and position using the Unix sort command. For a detailed list of different options available, please refer to the official docs of: diff --git a/nextflow.config b/nextflow.config index 7031af80..fce43369 100644 --- a/nextflow.config +++ b/nextflow.config @@ -317,7 +317,7 @@ manifest { ], [ name: 'Edmund Miller', - affiliation: 'Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, 800 W Campbell Rd, Richardson, TX 75080, USA', + affiliation: 'Department of Biological Sciences and Center for Systems Biology, University of Texas at Dallas, Texas, USA', email: 'nf-core@edmundmiller.dev', github: 'https://github.com/edmundmiller', contribution: ['maintainer', 'contributor'], // List of contribution types ('author', 'maintainer' or 'contributor')