Clear TODOs

oist · May 8, 2024 · b044e01 · b044e01
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diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -15,7 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -39,7 +39,6 @@ jobs:
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 </h1>
 
 [![GitHub Actions CI Status](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/ci.yml)
-[![GitHub Actions Linting Status](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pairgenomealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions Linting Status](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pairgenomealign/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pairgenomealign/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi:zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)

diff --git a/docs/output.md b/docs/output.md
@@ -2,42 +2,18 @@
 
 ## Introduction
 
-This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
+This document describes the output produced by the pipeline. Most of the plots are taken from the Last_dotplot report, which summarises results at the end of the pipeline.
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
 
 ## Pipeline overview
 
 The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps:
 
-- [FastQC](#fastqc) - Raw read QC
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
-### FastQC
-
-<details markdown="1">
-<summary>Output files</summary>
-
-- `fastqc/`
-  - `*_fastqc.html`: FastQC report containing quality metrics.
-  - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images.
-
-</details>
-
-[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/).
-
-![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png)
-
-![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png)
-
-![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
-
-:::note
-The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
-:::
 
 ### MultiQC
 

diff --git a/docs/usage.md b/docs/usage.md
@@ -6,8 +6,6 @@
 
 ## Introduction
 
-<!-- TODO nf-core: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website. -->
-
 ## Samplesheet input
 
 You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below.

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -13,7 +13,13 @@
             "properties": {
                 "seed": {
                     "type": "string",
-                    "enum": ["YASS", "NEAR", "MAM8", "RY128", "PSEUDO"],
+                    "enum": [
+                        "YASS",
+                        "NEAR",
+                        "MAM8",
+                        "RY128",
+                        "PSEUDO"
+                    ],
                     "help_text": "--seed selects the name of the LAST seed The default (YASS) searches for \u201clong-and-weak similarities\u201d that \u201callow for mismatches but not gaps\u201d. Among alternatives, there are NEAR for \u201cshort-and-strong (near-identical) similarities \u2026 with many gaps (insertions and deletions)\u201d, MAM8 to find \u201cweak similarities with high sensitivity, but low speed and high memory usage\u201d or RY128 that \u201creduces run time and memory use, by only seeking seeds at ~1/128 of positions in each sequence\u201d, which is useful when the purpose of running this pipeline is only to generate whole-genome dotplots, or when sensitivity for tiny fragments may be unnecessary or undesirable. Setting the seed to PSEUDO triggers protein-to-DNA alignment mode (experimental).",
                     "description": "The default (YASS) searches for \u201clong-and-weak similarities\u201d that \u201callow for mismatches but not gaps\u201d.",
                     "default": "YASS"
@@ -33,16 +39,20 @@
             "default": "",
             "properties": {
                 "skip_dotplot_o2m": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "To skip the dot plots representation of one to many alignment points"
                 },
                 "skip_dotplot_o2o": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "To skip the dot plots representation of one to one alignment points"
                 },
                 "skip_dotplot_m2o": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "To skip the dot plots representation of many to one alignment points"
                 },
                 "skip_dotplot_m2m": {
-                    "type": "boolean"
+                    "type": "boolean",
+                    "description": "To skip the dot plots representation of many to many alignment points"
                 }
             },
             "help_text": "Use --skip_dotplot_m2m, --skip_dotplot_m2o, --skip_dotplot_o2o --skip_dotplot_o2m to skip the production of the dot plots that can be computationally expensive and visually uninformative on large genomes with shared repeats."
@@ -52,7 +62,11 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "target", "outdir"],
+            "required": [
+                "input",
+                "target",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -231,7 +245,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -341,4 +362,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}