From 0eb2f035939c72e01d2f61d8fb2ded5c0b27128d Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Fri, 17 Jan 2025 15:11:46 +0100 Subject: [PATCH 1/5] Bump version after release --- .nf-core.yml | 10 +++++----- assets/multiqc_config.yml | 7 ++++--- nextflow.config | 2 +- ro-crate-metadata.json | 26 +++++++++++++------------- 4 files changed, 23 insertions(+), 22 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index aca765b..4142ed5 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,7 @@ lint: files_exist: - - conf/igenomes.config - - conf/igenomes_ignored.config + - conf/igenomes.config + - conf/igenomes_ignored.config nf_core_version: 3.1.1 repository_type: pipeline template: @@ -14,6 +14,6 @@ template: org: nf-core outdir: . skip_features: - - igenomes - - fastqc - version: 1.0.0 + - igenomes + - fastqc + version: 1.1.0dev diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 13dd96a..8840532 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,8 @@ report_comment: > - This report has been generated by the nf-core/rangeland - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/rangeland analysis pipeline. For information about how + to interpret these results, please see the documentation. report_section_order: "nf-core-rangeland-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3f7ff40..5c198c1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -277,7 +277,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '1.0.0' + version = '1.1.0dev' doi = '' } diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 19a1c1f..694b4ff 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -21,9 +21,9 @@ { "@id": "./", "@type": "Dataset", - "creativeWorkStatus": "Stable", - "datePublished": "2024-12-20T14:45:52+00:00", - "description": "

\n \n \n $\"nf-core/rangeland\"$ \n \n

[![GitHub Actions CI Status](https://github.com/nf-core/rangeland/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rangeland/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/rangeland/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rangeland/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/rangeland/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/rangeland)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23rangeland-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/rangeland)[![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/rangeland** is a geographical best-practice analysis pipeline for remotely sensed imagery.\nThe pipeline processes satellite imagery alongside auxiliary data in multiple steps to arrive at a set of trend files related to land-cover changes. The main pipeline steps are:\n\n1. Read satellite imagery, digital elevation model (dem), endmember definition, water vapor database (wvdb), datacube definition and area of interest definition (aoi)\n2. Generate allow list and analysis mask to determine which pixels from the satellite data can be used\n3. Preprocess data to obtain atmospherically corrected images alongside quality assurance information (aka. level 2 analysis read data)\n4. Merge spatially and temporally overlapping preprocessed data\n5. Classify pixels by applying linear spectral unmixing\n6. Time series analyses to obtain trends in vegetation dynamics to derive level 3 data\n7. Create mosaic and pyramid visualizations of the results\n8. Version reporting with MultiQC ([`MultiQC`](http://multiqc.info/))\n\n

\n $\"nf-core/rangeland$ \n

\n \n \n $\"nf-core/rangeland\"$ \n \n

\n $\"nf-core/rangeland$ \n

\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\nTo run, satellite imagery, water vapor data, a digital elevation model, endmember definitions, a datacube specification, and a area-of-interest specification are required as input data.\nPlease refer to the [usage documentation](https://nf-co.re/rangeland/usage) for details on the input structure.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/rangeland \\\n -profile \\\n --input \\\n --dem \\\n --wvdb \\\n --data_cube \\\n --aoi \\\n --endmember \\\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/rangeland/usage) and the [parameter documentation](https://nf-co.re/rangeland/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/rangeland/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/rangeland/output).\n\n## Credits\n\nThe rangeland workflow was originally written by:\n\n- [Fabian Lehmann](https://github.com/Lehmann-Fabian)\n- [David Frantz](https://github.com/davidfrantz)\n\nThe original workflow can be found on [github](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland).\n\nTransformation to nf-core/rangeland was conducted by [Felix Kummer](https://github.com/Felix-Kummer).\nnf-core alignment started on the [nf-core branch of the original repository](https://github.com/CRC-FONDA/FORCE2NXF-Rangeland/tree/nf-core).\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Fabian Lehmann](https://github.com/Lehmann-Fabian)\n- [Katarzyna Ewa Lewinska](https://github.com/kelewinska).\n\n## Acknowledgements\n\nThis pipeline was developed and aligned with nf-core as part of the [Foundations of Workflows for Large-Scale Scientific Data Analysis (FONDA)](https://fonda.hu-berlin.de/) initiative.\n\n[![FONDA](docs/images/fonda_logo2_cropped.png)](https://fonda.hu-berlin.de/)\n\nFONDA can be cited as follows:\n\n> **The Collaborative Research Center FONDA.**\n>\n> Ulf Leser, Marcus Hilbrich, Claudia Draxl, Peter Eisert, Lars Grunske, Patrick Hostert, Dagmar Kainm\u00fcller, Odej Kao, Birte Kehr, Timo Kehrer, Christoph Koch, Volker Markl, Henning Meyerhenke, Tilmann Rabl, Alexander Reinefeld, Knut Reinert, Kerstin Ritter, Bj\u00f6rn Scheuermann, Florian Schintke, Nicole Schweikardt, Matthias Weidlich.\n>\n> _Datenbank Spektrum_ 2021 doi: [10.1007/s13222-021-00397-5](https://doi.org/10.1007/s13222-021-00397-5)\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 `#rangeland` channel](https://nfcore.slack.com/channels/rangeland) (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\nThis pipeline is based one the publication listed below.\nThe publication can be cited as follows:\n\n> **FORCE on Nextflow: Scalable Analysis of Earth Observation Data on Commodity Clusters**\n>\n> [Lehmann, F., Frantz, D., Becker, S., Leser, U., Hostert, P. (2021). FORCE on Nextflow: Scalable Analysis of Earth Observation Data on Commodity Clusters. In CIKM Workshops.](https://www.informatik.hu-berlin.de/de/forschung/gebiete/wbi/research/publications/2021/force_nextflow.pdf/@@download/file/force_nextflow.pdf)\n", "hasPart": [ { "@id": "main.nf" @@ -105,7 +105,7 @@ }, "mentions": [ { - "@id": "#ef20dac5-c495-414e-b454-5262623b063f" + "@id": "#982c1a5b-c6b5-40dd-9654-64d0662525e6" } ], "name": "nf-core/rangeland" @@ -134,11 +134,11 @@ ], "creator": [ { - "@id": "#felix.kummer@hu-berlin.de" + "@id": "https://orcid.org/0009-0007-1154-6980" } ], "dateCreated": "", - "dateModified": "2024-12-20T15:45:52Z", + "dateModified": "2025-01-17T15:03:17Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -155,7 +155,7 @@ ], "maintainer": [ { - "@id": "#felix.kummer@hu-berlin.de" + "@id": "https://orcid.org/0009-0007-1154-6980" } ], "name": [ @@ -169,10 +169,10 @@ }, "url": [ "https://github.com/nf-core/rangeland", - "https://nf-co.re/rangeland/1.0.0/" + "https://nf-co.re/rangeland/dev/" ], "version": [ - "1.0.0" + "1.1.0dev" ] }, { @@ -188,11 +188,11 @@ "version": "!>=24.04.2" }, { - "@id": "#ef20dac5-c495-414e-b454-5262623b063f", + "@id": "#982c1a5b-c6b5-40dd-9654-64d0662525e6", "@type": "TestSuite", "instance": [ { - "@id": "#c395eb9b-579d-4fe8-9f81-fcb8eb9226b8" + "@id": "#29cb815b-c065-4520-a685-56de89aa859f" } ], "mainEntity": { @@ -201,7 +201,7 @@ "name": "Test suite for nf-core/rangeland" }, { - "@id": "#c395eb9b-579d-4fe8-9f81-fcb8eb9226b8", + "@id": "#29cb815b-c065-4520-a685-56de89aa859f", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/rangeland", "resource": "repos/nf-core/rangeland/actions/workflows/ci.yml", @@ -340,7 +340,7 @@ "url": "https://nf-co.re/" }, { - "@id": "#felix.kummer@hu-berlin.de", + "@id": "https://orcid.org/0009-0007-1154-6980", "@type": "Person", "email": "felix.kummer@hu-berlin.de", "name": "Felix Kummer" From 1a9c45c0dccdaa4c6f54646c45959b9cd4daaaf7 Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Fri, 17 Jan 2025 15:11:58 +0100 Subject: [PATCH 2/5] Update changelog --- CHANGELOG.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 313cdac..ea7c735 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,3 +15,13 @@ This work is a continuation, and nf-core port, of the [original version of this ### `Dependencies` ### `Deprecated` + +## v1.1.0dev - [date] + +### `Added` + +### `Fixed` + +### `Dependencies` + +### `Deprecated` From 25cf117798e624e416c8b93913296642297e7c5a Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Fri, 17 Jan 2025 15:27:15 +0100 Subject: [PATCH 3/5] Updated Zenodo information --- README.md | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 3e1db21..b884b8d 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,7 @@

[![GitHub Actions CI Status](https://github.com/nf-core/rangeland/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/rangeland/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/rangeland/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rangeland/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/rangeland/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/rangeland/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rangeland/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/rangeland/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.14679189-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.14679189) [![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%A524.04.2-23aa62.svg)](https://www.nextflow.io/) @@ -105,8 +105,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If you use nf-core/rangeland for your analysis, please cite it using the following doi: [10.5281/zenodo.14679189](https://doi.org/10.5281/zenodo.14679189) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. From d54caf303b1e67d9dd0492ef8e2cf00327ab29dd Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Fri, 17 Jan 2025 15:44:14 +0100 Subject: [PATCH 4/5] fixed linter error --- .nf-core.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 4142ed5..d4a9b40 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,7 +1,7 @@ lint: files_exist: - - conf/igenomes.config - - conf/igenomes_ignored.config + - conf/igenomes.config + - conf/igenomes_ignored.config nf_core_version: 3.1.1 repository_type: pipeline template: @@ -14,6 +14,6 @@ template: org: nf-core outdir: . skip_features: - - igenomes - - fastqc + - igenomes + - fastqc version: 1.1.0dev From 7b7a83eb38fe6637b647b4d9498fb005bfca2df8 Mon Sep 17 00:00:00 2001 From: Felix Kummer Date: Sun, 19 Jan 2025 10:39:26 +0100 Subject: [PATCH 5/5] Added missing doi entry --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 5c198c1..9df08cf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -278,7 +278,7 @@ manifest { defaultBranch = 'master' nextflowVersion = '!>=24.04.2' version = '1.1.0dev' - doi = '' + doi = 'https://doi.org/10.5281/zenodo.14679189' } // Nextflow plugins

\n \n \n \n \n

\n \n \n \n \n

\n \n \n $\"nf-core/rangeland\"$ \n \n

\n \n \n $\"nf-core/rangeland\"$ \n \n