Merge pull request #2 from sanger-tol/dev

Dev

Author: weaglesBio

.github/workflows/nf-test.yml

@@ -116,7 +116,7 @@ jobs:
   confirm-pass:
     needs: [nf-test]
     if: always()
-    runs-on:  # use GitHub runners
+    runs-on: # use GitHub runners
       - "ubuntu-latest"
     steps:
       - name: One or more tests failed (excluding latest-everything)

.pre-commit-config.yaml

@@ -15,13 +15,16 @@ repos:
               .*ro-crate-metadata.json$|
               modules/nf-core/.*|
               subworkflows/nf-core/.*|
-              .*\.snap$
+              .*\.snap$|
+              .*\.hmm$|
+              .*\.cm$
           )$
       - id: end-of-file-fixer
         exclude: |
           (?x)^(
               .*ro-crate-metadata.json$|
               modules/nf-core/.*|
               subworkflows/nf-core/.*|
-              .*\.snap$
+              .*\.snap$|
+              .*\.svg$
           )$

CITATION.cff

@@ -0,0 +1,29 @@
+authors:
+  - affiliation: Wellcome Sanger Institute
+    email: jd42@sanger.ac.uk
+    family-names: Downie
+    given-names: Jim
+    orcid: https://orcid.org/0000-0002-7175-0533
+    website: https://github.com/prototaxites
+  - affiliation: Wellcome Sanger Institute
+    email: we3@sanger.ac.uk
+    family-names: Eagles
+    given-names: Will
+    orcid: https://orcid.org/0009-0006-9956-0404
+    website: https://github.com/weaglesbio
+  - affiliation: Wellcome Sanger Institute
+    email: yy5@sanger.ac.uk
+    family-names: Sims
+    given-names: Yumi
+    orcid: https://orcid.org/0000-0003-4765-4872
+    website: https://github.com/yumisims
+cff-version: 1.2.0
+date-released: "2025-08-25"
+license: MIT
+message: If you use this software, please cite it using the metadata from this file
+  and all references from CITATIONS.md .
+repository-code: https://github.com/sanger-tol/nfmicrofinder
+title: sanger-tol/nfmicrofinder v1.0.0
+type: software
+url: https://pipelines.tol.sanger.ac.uk/nfmicrofinder
+version: 1.0.0

CITATIONS.md

@@ -10,10 +10,6 @@
 
 ## Pipeline tools
 
-
-
-
-
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)

README.md

@@ -1,87 +1,78 @@
-# sanger-tol/nfmicrofinder
+# nf-core/nfmicrofinder
 
-[![GitHub Actions CI Status](https://github.com/sanger-tol/nfmicrofinder/actions/workflows/nf-test.yml/badge.svg)](https://github.com/sanger-tol/nfmicrofinder/actions/workflows/nf-test.yml)
-[![GitHub Actions Linting Status](https://github.com/sanger-tol/nfmicrofinder/actions/workflows/linting.yml/badge.svg)](https://github.com/sanger-tol/nfmicrofinder/actions/workflows/linting.yml)[![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 CI Status](https://github.com/nf-core/nfmicrofinder/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/nfmicrofinder/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/nfmicrofinder/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/nfmicrofinder/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/nfmicrofinder/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/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/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
-[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
+[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.1-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.1)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/sanger-tol/nfmicrofinder)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/nfmicrofinder)
 
-## Introduction
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23nfmicrofinder-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/nfmicrofinder)[![Follow on Bluesky](https://img.shields.io/badge/bluesky-%40nf__core-1185fe?labelColor=000000&logo=bluesky)](https://bsky.app/profile/nf-co.re)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
-**sanger-tol/nfmicrofinder** is a bioinformatics pipeline that ...
+## Introduction
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+**nf-core/nfmicrofinder** is a bioinformatics pipeline that aids in the curation of bird genome assemblies by identifying putative microchromosome scaffolds and moving them to the start of the genome assembly FASTA file.
 
-<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
-     workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.
 
-## Usage
+## Pipeline Summary
 
-> [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+1.  Input validation and parameter checks
+2.  Index reference genome using Miniprot
+3.  Align protein sequences to genome using Miniprot
+4.  Filter alignments based on quality thresholds (identity ≥70%, score ≥60)
+5.  Sort FASTA file based on filtered alignments to prioritize microchromosomes
+6.  Generate final reordered assembly and pipeline reports
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
+## Quick Start
 
-First, prepare a samplesheet with your input data that looks as follows:
+1.  Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=24.10.5`)
 
-`samplesheet.csv`:
+2.  Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
 
-```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
-```
+3.  Download the pipeline and test it on a minimal dataset with a single command:
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+    ```bash
+    nextflow run main.nf -profile test,docker
+    ```
 
--->
+    > Note that it is recommend to use the `-profile` parameter to specify the container technology of your choice. See the [nf-core pipeline documentation](https://nf-co.re/usage/running#software-dependencies) for more information.
 
-Now, you can run the pipeline using:
+4.  Start running your own analysis!
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+    ```bash
+    nextflow run main.nf \
+        --input genome.fa \
+        --pep_file proteins.fa \
+        --output_prefix my_analysis \
+        --outdir <OUTDIR>
+    ```
 
-```bash
-nextflow run sanger-tol/nfmicrofinder \
-   -profile <docker/singularity/.../institute> \
-   --input samplesheet.csv \
-   --outdir <OUTDIR>
-```
+## Documentation
 
-> [!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).
+The nfmicrofinder pipeline comes with documentation about the pipeline [usage](docs/usage.md) and [output](docs/output.md).
 
 ## Credits
 
-sanger-tol/nfmicrofinder was originally written by yumisims.
+nfmicrofinder was originally written by Yumi Sims and Will Eagle ([@weaglesBio](https://github.com/weaglesBio)).
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- Jim Downie ([@prototaxites](https://github.com/prototaxites))
 
 ## Contributions and Support
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use sanger-tol/nfmicrofinder for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
-
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
-This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
+You can cite the `nf-core` publication as follows:
 
 > **The nf-core framework for community-curated bioinformatics pipelines.**
 >

bin/sort_fasta.rb

@@ -0,0 +1,57 @@
+#!/usr/bin/env ruby
+# frozen_string_literal: true
+
+# usage: ruby sort_fasta.rb -o <id-tab-int> -f <FASTA> [ -l <length> ]
+
+require 'gdbm'
+require 'tempfile'
+require 'yaml'
+require 'bio'
+require 'optparse'
+
+
+Version = '1.1'
+
+options = {}
+OptionParser.new do |opts|
+  opts.banner = 'Usage: sort_fasta.rb [options]'
+
+  opts.on('-f FASTA', '--fasta FASTA', String, 'FASTA file')
+  opts.on('-o TSV', '--order TSV', String, 'TSV file with sort order')
+  opts.on('-l', '--length_cutoff LEN', Integer, 'sequences > LEN bp will not be sorted')
+  opts.on('-m', '--minimum_length MIN', Integer, 'sequences < MIN bp will not be sorted')
+  opts.on('-v', '--version', 'Prints version') do
+    puts $0+ ': ' + opts.version
+    exit
+  end
+end.parse!(into: options)
+
+dbfile = 'seqstore.db'
+gdb = GDBM.new(dbfile, nil, GDBM::NEWDB)
+
+id_to_count = {}
+File.open(options[:order]).each do |line|
+  (id, count) = line.chomp.split
+  id_to_count[id] = count.to_i
+end
+
+id_to_size = {}
+Bio::FlatFile.open(Bio::FastaFormat, options[:fasta]) do |ff|
+  ff.each do |entry|
+    id_to_count[entry.entry_id] ||= 0
+    id_to_count[entry.entry_id] = 0 if options[:length_cutoff] && entry.length > options[:length_cutoff]
+    id_to_count[entry.entry_id] = 0 if options[:minimum_length] && entry.length < options[:minimum_length]
+    id_to_size[entry.entry_id] = entry.seq.size
+    gdb[entry.entry_id] = entry.to_yaml
+  end
+end
+
+gdb.keys.sort_by  do |e|
+  [id_to_count[e], id_to_size[e]]
+end.reverse.each  do |id|
+  e = YAML.safe_load(gdb[id], permitted_classes: [Bio::FastaFormat, Bio::FastaDefline, Bio::Sequence::Generic])
+  puts e.seq.to_fasta(e.definition)
+end
+
+gdb.close
+File.delete(dbfile)

conf/modules.config

@@ -18,4 +18,10 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
+
+    withName: 'MINIPROT_ALIGN' {
+        ext.prefix = { "${meta.id}_aligned" }
+        ext.args   = { "--gff -u" }
+    }
+
 }

conf/test.config

@@ -23,7 +23,6 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+    output_prefix = "test"
 }

conf/test_full.config

@@ -13,12 +13,6 @@
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
-
-    // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
-
-    // Fasta references
-    fasta = params.pipelines_testdata_base_path + 'viralrecon/genome/NC_045512.2/GCF_009858895.2_ASM985889v3_genomic.200409.fna.gz'
+    input = 'https://tolit.cog.sanger.ac.uk/test-data/Aythya_fuligula/assembly/bAytFul3.fa.gz'
+    output_prefix = 'bAytFul3'
 }

docs/README.md

@@ -1,8 +1,10 @@
-# sanger-tol/nfmicrofinder: Documentation
+# nf-core/nfmicrofinder: Documentation
 
-The sanger-tol/nfmicrofinder documentation is split into the following pages:
+The nf-core/nfmicrofinder documentation is split into the following pages:
 
 - [Usage](usage.md)
   - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags.
 - [Output](output.md)
   - An overview of the different results produced by the pipeline and how to interpret them.
+
+You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re)