diff --git a/.editorconfig b/.editorconfig index 72dda28..6d9b74c 100644 --- a/.editorconfig +++ b/.editorconfig @@ -31,3 +31,7 @@ indent_size = unset # ignore python and markdown [*.{py,md}] indent_style = unset + +# ignore ro-crate metadata files +[**/ro-crate-metadata.json] +insert_final_newline = unset diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index fd434ef..f4a807b 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -9,7 +9,6 @@ body: - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [nf-core/fastqrepair pipeline documentation](https://nf-co.re/fastqrepair/usage) - - type: textarea id: description attributes: diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 353abae..f733ec0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs). Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release. -Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/fastqrepair/tree/master/.github/CONTRIBUTING.md) +Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/fastqrepair/tree/main/.github/CONTRIBUTING.md) --> ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fastqrepair/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/fastqrepair/tree/main/.github/CONTRIBUTING.md) - [ ] If necessary, also make a PR on the nf-core/fastqrepair _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core pipelines lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml index 2576cc0..13b51e2 100644 --- a/.github/workflows/download_pipeline.yml +++ b/.github/workflows/download_pipeline.yml @@ -28,8 +28,12 @@ env: NXF_ANSI_LOG: false jobs: - download: + configure: runs-on: ubuntu-latest + outputs: + REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }} + REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }} + REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }} steps: - name: Install Nextflow uses: nf-core/setup-nextflow@v2 @@ -53,22 +57,27 @@ jobs: pip install git+https://github.com/nf-core/tools.git@dev - name: Get the repository name and current branch set as environment variable + id: get_repo_properties run: | - echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV} - echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV} - echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV} + echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT" + echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT" + echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT" - name: Make a cache directory for the container images run: | mkdir -p ./singularity_container_images + download: + runs-on: ubuntu-latest + needs: configure + steps: - name: Download the pipeline env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images run: | - nf-core pipelines download ${{ env.REPO_LOWERCASE }} \ - --revision ${{ env.REPO_BRANCH }} \ - --outdir ./${{ env.REPOTITLE_LOWERCASE }} \ + nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \ + --revision ${{ needs.configure.outputs.REPO_BRANCH }} \ + --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \ --compress "none" \ --container-system 'singularity' \ --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \ @@ -76,14 +85,14 @@ jobs: --download-configuration 'yes' - name: Inspect download - run: tree ./${{ env.REPOTITLE_LOWERCASE }} + run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} - name: Count the downloaded number of container images id: count_initial run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Initial container image count: $image_count" - echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT" - name: Run the downloaded pipeline (stub) id: stub_run_pipeline @@ -91,27 +100,27 @@ jobs: env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results + run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results - name: Run the downloaded pipeline (stub run not supported) id: run_pipeline - if: ${{ job.steps.stub_run_pipeline.status == failure() }} + if: ${{ steps.stub_run_pipeline.outcome == 'failure' }} env: NXF_SINGULARITY_CACHEDIR: ./singularity_container_images NXF_SINGULARITY_HOME_MOUNT: true - run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results + run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results - name: Count the downloaded number of container images id: count_afterwards run: | image_count=$(ls -1 ./singularity_container_images | wc -l | xargs) echo "Post-pipeline run container image count: $image_count" - echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV} + echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT" - name: Compare container image counts run: | - if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then - initial_count=${{ env.IMAGE_COUNT_INITIAL }} - final_count=${{ env.IMAGE_COUNT_AFTER }} + if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then + initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }} + final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }} difference=$((final_count - initial_count)) echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!" tree ./singularity_container_images diff --git a/.nf-core.yml b/.nf-core.yml index cf21732..b327f9d 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -10,5 +10,5 @@ template: org: nf-core outdir: . skip_features: - - igenomes + - igenomes version: 1.0.0 diff --git a/.prettierignore b/.prettierignore index 437d763..edd29f0 100644 --- a/.prettierignore +++ b/.prettierignore @@ -10,3 +10,4 @@ testing/ testing* *.pyc bin/ +ro-crate-metadata.json diff --git a/CITATIONS.md b/CITATIONS.md index c80c1da..f89b622 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -12,9 +12,7 @@ - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) -> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. - -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. diff --git a/LICENSE b/LICENSE index 49b5de7..c75ab34 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) Tommaso Mazza +Copyright (c) The nf-core/fastqrepair team Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/README.md b/README.md index 27e7b3f..5544d16 100644 --- a/README.md +++ b/README.md @@ -3,9 +3,7 @@ nf-core/fastqrepair - - -[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml) +[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml) [![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/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) @@ -29,15 +27,12 @@ - - -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!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. +> 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. - - - + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/nf-core-fastqrepair_logo_light.png b/assets/nf-core-fastqrepair_logo_light.png index ecb43c5..f0d28a1 100644 Binary files a/assets/nf-core-fastqrepair_logo_light.png and b/assets/nf-core-fastqrepair_logo_light.png differ diff --git a/assets/schema_input.json b/assets/schema_input.json index 5a255aa..f790b40 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/master/assets/schema_input.json", + "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/main/assets/schema_input.json", "title": "nf-core/fastqrepair pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", diff --git a/conf/test.config b/conf/test.config index 1491377..688c289 100644 --- a/conf/test.config +++ b/conf/test.config @@ -26,6 +26,4 @@ params { // 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' - - } diff --git a/docs/images/nf-core-fastqrepair_logo_dark.png b/docs/images/nf-core-fastqrepair_logo_dark.png index ebb0aa4..893a206 100644 Binary files a/docs/images/nf-core-fastqrepair_logo_dark.png and b/docs/images/nf-core-fastqrepair_logo_dark.png differ diff --git a/docs/images/nf-core-fastqrepair_logo_light.png b/docs/images/nf-core-fastqrepair_logo_light.png index 8253ec1..3523d7e 100644 Binary files a/docs/images/nf-core-fastqrepair_logo_light.png and b/docs/images/nf-core-fastqrepair_logo_light.png differ diff --git a/docs/output.md b/docs/output.md index 52885ed..44759a9 100644 --- a/docs/output.md +++ b/docs/output.md @@ -12,8 +12,7 @@ The directories listed below will be created in the results directory after the 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 +- [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 @@ -27,9 +26,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d -[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](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
Output files @@ -43,9 +40,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . - -### Pipeline information +Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see .### Pipeline information
Output files diff --git a/docs/usage.md b/docs/usage.md index bc464d9..704a23c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -129,7 +129,7 @@ Several generic profiles are bundled with the pipeline which instruct the pipeli > [!IMPORTANT] > We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. -The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is suported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). +The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to check if your system is supported, please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). Note that multiple profiles can be loaded, for example: `-profile test,docker` - the order of arguments is important! They are loaded in sequence, so later profiles can overwrite earlier profiles. diff --git a/nextflow.config b/nextflow.config index 3380332..b8094fb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,7 +235,7 @@ manifest { 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""" mainScript = 'main.nf' - defaultBranch = 'master' + defaultBranch = 'main' nextflowVersion = '!>=24.04.2' version = '1.0.0' doi = '' @@ -269,7 +269,7 @@ validation { https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/nf-core/fastqrepair/blob/master/CITATIONS.md + https://github.com/nf-core/fastqrepair/blob/main/CITATIONS.md """ } summary { @@ -277,3 +277,6 @@ validation { afterText = validation.help.afterText } } + +// Load modules.config for DSL2 module specific options +includeConfig 'conf/modules.config' diff --git a/nextflow_schema.json b/nextflow_schema.json index d38468b..bfcd08c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/master/nextflow_schema.json", + "$id": "https://raw.githubusercontent.com/nf-core/fastqrepair/main/nextflow_schema.json", "title": "nf-core/fastqrepair pipeline parameters", "description": "A pipeline to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving", "type": "object", @@ -193,7 +193,6 @@ { "$ref": "#/$defs/input_output_options" }, - { "$ref": "#/$defs/institutional_config_options" }, diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 1f59a7e..8047bcb 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "Stable", - "datePublished": "2024-12-12T11:23:42+00:00", - "description": "

\n \n \n \"nf-core/fastqrepair\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/fastqrepair)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fastqrepair-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fastqrepair)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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)\n\n## Introduction\n\n**nf-core/fastqrepair** is a bioinformatics pipeline that ...\n\n\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/fastqrepair \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/fastqrepair/usage) and the [parameter documentation](https://nf-co.re/fastqrepair/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/fastqrepair/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/fastqrepair/output).\n\n## Credits\n\nnf-core/fastqrepair was originally written by Tommaso Mazza.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#fastqrepair` channel](https://nfcore.slack.com/channels/fastqrepair) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2024-12-20T15:55:16+00:00", + "description": "

\n \n \n \"nf-core/fastqrepair\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fastqrepair/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/fastqrepair/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fastqrepair/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/fastqrepair/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![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/fastqrepair)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fastqrepair-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fastqrepair)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![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)\n\n## Introduction\n\n**nf-core/fastqrepair** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> 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.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/fastqrepair \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> 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).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/fastqrepair/usage) and the [parameter documentation](https://nf-co.re/fastqrepair/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/fastqrepair/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/fastqrepair/output).\n\n## Credits\n\nnf-core/fastqrepair was originally written by Tommaso Mazza.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#fastqrepair` channel](https://nfcore.slack.com/channels/fastqrepair) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" @@ -99,7 +99,7 @@ }, "mentions": [ { - "@id": "#6715f8f9-6acc-4edb-9e5f-04f8170eedcb" + "@id": "#e47dcf54-4468-4137-b17d-444991abfe42" } ], "name": "nf-core/fastqrepair" @@ -121,9 +121,13 @@ }, { "@id": "main.nf", - "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"], + "@type": [ + "File", + "SoftwareSourceCode", + "ComputationalWorkflow" + ], "dateCreated": "", - "dateModified": "2024-12-12T11:23:42Z", + "dateModified": "2024-12-20T16:55:16Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -139,16 +143,25 @@ "unpaired-reads", "well-formed" ], - "license": ["MIT"], - "name": ["nf-core/fastqrepair"], + "license": [ + "MIT" + ], + "name": [ + "nf-core/fastqrepair" + ], "programmingLanguage": { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow" }, "sdPublisher": { "@id": "https://nf-co.re/" }, - "url": ["https://github.com/nf-core/fastqrepair", "https://nf-co.re/fastqrepair/1.0.0/"], - "version": ["1.0.0"] + "url": [ + "https://github.com/nf-core/fastqrepair", + "https://nf-co.re/fastqrepair/1.0.0/" + ], + "version": [ + "1.0.0" + ] }, { "@id": "https://w3id.org/workflowhub/workflow-ro-crate#nextflow", @@ -163,11 +176,11 @@ "version": "!>=24.04.2" }, { - "@id": "#6715f8f9-6acc-4edb-9e5f-04f8170eedcb", + "@id": "#e47dcf54-4468-4137-b17d-444991abfe42", "@type": "TestSuite", "instance": [ { - "@id": "#9642e118-a6cd-43e3-b4a6-7f24684f7b33" + "@id": "#e9ee0c63-7454-4a9c-963c-7fe00f63a406" } ], "mainEntity": { @@ -176,7 +189,7 @@ "name": "Test suite for nf-core/fastqrepair" }, { - "@id": "#9642e118-a6cd-43e3-b4a6-7f24684f7b33", + "@id": "#e9ee0c63-7454-4a9c-963c-7fe00f63a406", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/fastqrepair", "resource": "repos/nf-core/fastqrepair/actions/workflows/ci.yml", @@ -305,4 +318,4 @@ "url": "https://nf-co.re/" } ] -} +} \ No newline at end of file diff --git a/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf b/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf index c23e40f..c2e86ee 100644 --- a/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_fastqrepair_pipeline/main.nf @@ -112,7 +112,7 @@ workflow PIPELINE_COMPLETION { main: summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json") def multiqc_reports = multiqc_report.toList() - + // // Completion email and summary //