nf-core · mazzalab · Oct 27, 2024 · Oct 26, 2024 · Oct 26, 2024 · Oct 26, 2024
diff --git a/README.md b/README.md
@@ -52,23 +52,11 @@ Now, you can run the pipeline using:
 
 ```bash
 nextflow run nf-core/fastqrepair \
-   -profile <docker/singularity/.../institute> \
+   -profile <test/docker> \
    --input samplesheet.csv \
    --outdir <OUTDIR>
 ```
 
-optional parameters are:
-
-```txt
---chunk_size <int multiple of 4>
---qin <33/64>
---alphabet <ACGTN>
-```
-
-where
-
-> `chunk_size` is the number of lines of chunks of the original fastq file (caution! Too big or too small numbers may significantly impact on performance); `qin` is the ASCII offset (33=Sanger, 64=old Solexa); `alphabet` is the allowed alphabet in the SEQ line of the FASTQ file.
-
 > [!WARNING]
 > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).
 
@@ -84,10 +72,9 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/fastqrepair was designed and written by [Tommaso Mazza](https://github.com/mazzalab).
+`nf-core/fastqrepair` was designed and written by [Tommaso Mazza](https://github.com/mazzalab).
 
 <!-- We thank the following people for their extensive assistance in the development of this pipeline: -->
-
 <!-- nf-core: If applicable, make list of people who have also contributed -->
 
 ## Contributions and Support

diff --git a/assets/email_template.html b/assets/email_template.html
@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/fastqrepair: A pipeline to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving">
+  <meta name="description" content="nf-core/fastqrepair: A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered">
   <title>nf-core/fastqrepair Pipeline Report</title>
 </head>
 <body>

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/fastqrepair/tree/dev" target="_blank">nf-core/fastqrepair</a>
+  This report has been generated by the <a href="https://github.com/nf-core/fastqrepair/releases/tag/1.0.0" target="_blank">nf-core/fastqrepair</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/fastqrepair/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/fastqrepair/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-fastqrepair-methods-description":
     order: -1000

diff --git a/docs/usage.md b/docs/usage.md
@@ -54,7 +54,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/fastqrepair --input ./samplesheet.csv --outdir ./results -profile docker
+nextflow run nf-core/fastqrepair --input samplesheet.csv --outdir ./results -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -85,22 +85,12 @@ nextflow run nf-core/fastqrepair -profile docker -params-file params.yaml
 with:
 
 ```yaml title="params.yaml"
-input: './samplesheet.csv'
-outdir: './results/'
-<...>
+## Mandatory params
+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
-```
-
-> [!WARNING]
-> Caution! Too big or too small `chunk size` numbers may significantly impact on performance
-> :::
+Optional parameters are described in the [Parameters](https://nf-co.re/fastqrepair/dev/parameters/) tab.
 
 You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch).
 
@@ -158,7 +148,7 @@ 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/)
@@ -171,7 +161,7 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof
 - `wave`
   - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later).
 - `conda`
-  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. -->
+  - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer.
 
 ### `-resume`
 

diff --git a/nextflow.config b/nextflow.config
@@ -14,7 +14,7 @@ params {
 
     // Boilerplate options
     outdir                       = null
-    chunk_size                   = 3000
+    chunk_size                   = 20000000
     qin                          = 33
     alphabet                     = "ACGTN"
 
@@ -155,7 +155,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa
 
 // Load nf-core/fastqrepair custom profiles from different institutions.
 // REMIND for the future: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/fastqrepair.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/fastqrepair.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -214,10 +214,10 @@ manifest {
     name            = 'nf-core/fastqrepair'
     author          = """Tommaso Mazza"""
     homePage        = 'https://github.com/nf-core/fastqrepair'
-    description     = """A pipeline to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving"""
+    description     = """A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -2,7 +2,7 @@
     "$schema": "https://json-schema.org/draft/2020-12/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/master/nextflow_schema.json",
     "title": "nf-core/fastqrepair pipeline parameters",
-    "description": "A pipeline to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving",
+    "description": "A pipeline that can be used to recover corrupted FASTQ.gz files, drop or fix uncompliant reads, remove unpaired reads, and settles reads that became disordered",
     "type": "object",
     "$defs": {
         "input_output_options": {
@@ -26,22 +26,27 @@
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",
-                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "description": "The output directory where the results will be saved.",
+                    "help_text": "You have to use absolute paths to storage on Cloud infrastructure.",
                     "fa_icon": "fas fa-folder-open"
                 },
                 "chunk_size": {
                     "type": "integer",
+                    "default": 20000000,
                     "description": "The input fastq file will be split into chunks of this numnber of lines to speedup wiping. The number must be multiple of 4.",
                     "fa_icon": "fas fa-puzzle-piece"
                 },
                 "qin": {
                     "type": "integer",
+                    "enum": [33, 64],
+                    "default": 33,
                     "description": "the ASCII offset (33=Sanger, 64=old Solexa).",
                     "fa_icon": "fas fa-puzzle-piece"
                 },
                 "alphabet": {
                     "type": "string",
-                    "description": "Allowed character in the SEQ line. Default: ACGTN.",
+                    "default": "ACGTN",
+                    "description": "Allowed character in the SEQ line.",
                     "fa_icon": "fas fa-solid fa-arrows-left-right-to-line"
                 },
                 "email": {
@@ -112,7 +117,7 @@
                     "type": "boolean",
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
-                    "hidden": true
+                    "hidden": false
                 },
                 "publish_dir_mode": {
                     "type": "string",
@@ -125,11 +130,10 @@
                 },
                 "publish_dir_all_tools": {
                     "type": "boolean",
-                    "default": false,
                     "description": "To specify whether to publish all pipeline intermediate results to output directory.",
                     "help_text": "This option tells the pipeline whether to publish all intermediate results to output directory.",
                     "fa_icon": "fas fa-copy",
-                    "hidden": true
+                    "hidden": false
                 },
                 "email_on_fail": {
                     "type": "string",