From 1e054b020da2e33330cfb67add33d7add2c65c8d Mon Sep 17 00:00:00 2001
From: mazzalab <t.mazza@css-mendel.it>
Date: Thu, 24 Oct 2024 18:32:29 +0000
Subject: [PATCH] run prettier on MD files

---
 .devcontainer/devcontainer.json |  5 +----
 CHANGELOG.md                    | 15 ++++++++-------
 CITATIONS.md                    |  1 -
 docs/output.md                  |  2 +-
 docs/usage.md                   | 27 ++++++++++++++++-----------
 5 files changed, 26 insertions(+), 24 deletions(-)

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index 11d327c..d59947c 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -14,10 +14,7 @@
     },
     "customizations": {
         "vscode": {
-            "extensions": [
-                "ms-azuretools.vscode-docker",
-                "nf-core.nf-core-extensionpack"
-            ]
+            "extensions": ["ms-azuretools.vscode-docker", "nf-core.nf-core-extensionpack"]
         }
     },
     // "remoteEnv": {
diff --git a/CHANGELOG.md b/CHANGELOG.md
index f89ccba..4954f46 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,10 +8,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 Initial release of nf-core/fastqrepair, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Dependencies`
-| Dependency                      | New version |
-| ------------------------------- | ----------- |
-| `BBmap`                         | 39.08       |
-| `FastQC`                        | 0.12.1      |
-| `gzrt`                          | 0.8         |
-| `Trimmonatic`                   | 0.39        |
-| `FastqWiper`                    | 1.0.0       |
+
+| Dependency    | New version |
+| ------------- | ----------- |
+| `BBmap`       | 39.08       |
+| `FastQC`      | 0.12.1      |
+| `gzrt`        | 0.8         |
+| `Trimmonatic` | 0.39        |
+| `FastqWiper`  | 1.0.0       |
diff --git a/CITATIONS.md b/CITATIONS.md
index 2e4fbd5..26cb4fe 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -30,7 +30,6 @@
 
 > Bushnell B. (2024). BBMap [Online]
 
-
 ## Software packaging/containerisation tools
 
 <!-- - [Anaconda](https://anaconda.com)
diff --git a/docs/output.md b/docs/output.md
index 1b05b46..78e2988 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -34,6 +34,7 @@ The nf-core/fastqrepair pipeline is built using [Nextflow](https://www.nextflow.
 ```
 
 where
+
 - `mysampleA_R1_repaired.fastq.gz` and `mysampleA_R2_repaired.fastq.gz` are the repaired fastq files
 - `mysampleA_R1_report.txt` and `mysampleA_R2_report.txt` are the summaries of the cleaning task by [FastqWiper](#fastqwiper)
 - **QC** contains [FastQC](#fastqc) QC analysis results
@@ -52,7 +53,6 @@ where
 
 [FastqWiper](https://github.com/mazzalab/fastqwiper) is a Python package that makes an uncompliant FASTQ file well-formed by dropping and fixing pesky lines.
 
-
 ### FastQC
 
 <details markdown="1">
diff --git a/docs/usage.md b/docs/usage.md
index bf9543c..7071742 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -14,9 +14,10 @@ You will need to create a samplesheet that will be provided in input to `fastqre
 --input '[path to samplesheet file]'
 ```
 
- The samplesheet will contain information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
+The samplesheet will contain information about the samples you would like to analyse before running the pipeline. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.
 
 ### Multiple runs of the same sample
+
 > [!WARNING]
 > All `sample` identifiers in a samplesheet must be unique. Rows with different `sample` identifiers but same file names are not allowed either.
 
@@ -40,11 +41,11 @@ mysampleB,sample_2_R1.fastq.gz,sample_2_R2.fastq.gz
 mysampleC,sample_3_R1.fastq.gz,
 ```
 
-| Column    | Description                                                                                                                                                                            |
-| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `sample`  | Custom sample name. Spaces in sample names are automatically converted to underscores (`_`). |
-| `fastq_1` | Full path to FastQ file for short reads R1. Files can be gzipped or not, with the extensions: ".fastq.gz", ".fq.gz", or ".fastq".                                                             |
-| `fastq_2` | Full path to FastQ file for short reads R2 (optional). Files can be gzipped or not, with the extensions: ".fastq.gz", ".fq.gz", or ".fastq".                                                             |
+| Column    | Description                                                                                                                                  |
+| --------- | -------------------------------------------------------------------------------------------------------------------------------------------- |
+| `sample`  | Custom sample name. Spaces in sample names are automatically converted to underscores (`_`).                                                 |
+| `fastq_1` | Full path to FastQ file for short reads R1. Files can be gzipped or not, with the extensions: ".fastq.gz", ".fq.gz", or ".fastq".            |
+| `fastq_2` | Full path to FastQ file for short reads R2 (optional). Files can be gzipped or not, with the extensions: ".fastq.gz", ".fq.gz", or ".fastq". |
 
 An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline.
 
@@ -88,15 +89,18 @@ input: './samplesheet.csv'
 outdir: './results/'
 <...>
 ```
+
 optional parameters are:
+
 ```yaml title="optional_params.yaml"
-chunk_size: <int multiple of 4>   # number of lines in each chunk generated from the original fastq file
-qin:        <33/64>               # ASCII offset (33=Sanger, 64=old Solexa)
-alphabet:   <ACGTN>               # allowed alphabet in the SEQ line of the FASTQ file
+chunk_size: <int multiple of 4> # number of lines in each chunk generated from the original fastq file
+qin: <33/64> # ASCII offset (33=Sanger, 64=old Solexa)
+alphabet: <ACGTN> # allowed alphabet in the SEQ line of the FASTQ file
 ```
+
 > [!WARNING]
 > Caution! Too big or too small `chunk size` numbers may significantly impact on performance
-:::
+> :::
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
@@ -137,6 +141,7 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 <!-- :::info
 We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
 ::: -->
+
 :::info
 We highly recommend the use of Docker container for full pipeline reproducibility.
 :::
@@ -153,7 +158,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
   - Includes links to test data so needs no other parameters
 - `docker`
   - A generic configuration profile to be used with [Docker](https://docker.com/)
-<!-- - `singularity`
+  <!-- - `singularity`
   - A generic configuration profile to be used with [Singularity](https://sylabs.io/docs/)
 - `podman`
   - A generic configuration profile to be used with [Podman](https://podman.io/)