diff --git a/.nf-core.yml b/.nf-core.yml
index 50507a8..99a3e1e 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -13,7 +13,7 @@ repository_type: pipeline
template:
author: Olga Botvinnik, Evangelos Karatzas
description: Generation of sequence-level annotations for amino acid sequences
- version: 1.0.0
+ version: 1.1.0dev
force: true
outdir: .
skip_features:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6c034ab..cf18d44 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,8 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## v1.1.0dev - [date]
+
## v1.0.0 - Yellow Saiga - [2026/02/09]
Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template.
diff --git a/README.md b/README.md
index fb552f8..2eef432 100644
--- a/README.md
+++ b/README.md
@@ -7,7 +7,7 @@
[](https://github.com/codespaces/new/nf-core/proteinannotator)
[](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)
-[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)
+[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.18547735)
[](https://www.nf-test.com)
[](https://www.nextflow.io/)
@@ -99,8 +99,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
## Citations
-
-
+If you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)
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/multiqc_config.yml b/assets/multiqc_config.yml
index e9ddc17..c2f9fe5 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,5 +1,5 @@
report_comment: >
- This report has been generated by the nf-core/proteinannotator analysis pipeline. For information about how to interpret these results, please see the documentation.
+ This report has been generated by the nf-core/proteinannotator analysis pipeline. For information about how to interpret these results, please see the documentation.
report_section_order:
"nf-core-proteinannotator-methods-description":
order: -1000
diff --git a/nextflow.config b/nextflow.config
index e56f91f..d79a287 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -286,7 +286,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=25.10.0'
- version = '1.0.0'
+ version = '1.1.0dev'
doi = ''
}
diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
index 51bb9a3..936e72a 100644
--- a/ro-crate-metadata.json
+++ b/ro-crate-metadata.json
@@ -21,9 +21,9 @@
{
"@id": "./",
"@type": "Dataset",
- "creativeWorkStatus": "Stable",
- "datePublished": "2026-02-09T10:42:29+00:00",
- "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/proteinannotator)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.XXXXXXX)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[](https://nfcore.slack.com/channels/proteinannotator)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n
\n \n \n \n \n
\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)\n2. Functional annotation:\n - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/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/proteinannotator/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/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (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",
+ "creativeWorkStatus": "InProgress",
+ "datePublished": "2026-02-09T13:54:13+00:00",
+ "description": "
\n \n \n \n \n
\n\n[](https://github.com/codespaces/new/nf-core/proteinannotator)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/nf-test.yml)\n[](https://github.com/nf-core/proteinannotator/actions/workflows/linting.yml)[](https://nf-co.re/proteinannotator/results)[](https://doi.org/10.5281/zenodo.18547735)\n[](https://www.nf-test.com)\n\n[](https://www.nextflow.io/)\n[](https://github.com/nf-core/tools/releases/tag/3.5.1)\n[](https://docs.conda.io/en/latest/)\n[](https://www.docker.com/)\n[](https://sylabs.io/docs/)\n[](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/proteinannotator)\n\n[](https://nfcore.slack.com/channels/proteinannotator)[](https://bsky.app/profile/nf-co.re)[](https://mstdn.science/@nf_core)[](https://www.youtube.com/c/nf-core)\n\n## Introduction\n\n**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics for protein FASTA inputs and produces protein annotations based on predicted sequence features, including conserved domains, functions, and secondary structure.\n\n
\n \n \n \n \n
\n\n### Check quality and pre-process\n\nGenerate input amino acid sequence statistics with ([`SeqFu`](https://github.com/telatin/seqfu2/)) and pre-process them (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) with ([`SeqKit`](https://github.com/shenwei356/seqkit/))\n\n### Annotate sequences\n\n1. Conserved domain annotation with ([`hmmer`](https://github.com/EddyRivasLab/hmmer/)) against databases\n such as [Pfam](https://ftp.ebi.ac.uk/pub/databases/Pfam/) and [FunFam](https://download.cathdb.info/cath/releases/all-releases/)\n2. Functional annotation:\n - ([`InterProScan`](https://interproscan-docs.readthedocs.io/en/v5/)) a software tool used to analyze protein sequences by scanning them against the signatures of protein families, domains, and sites in the [InterPro](https://www.ebi.ac.uk/interpro/) database, helping to identify their functional characteristics.\n3. Predict secondary structure compositional features such as \u03b1-helices, \u03b2-strands and coils with ([`s4pred`](https://github.com/psipred/s4pred))\n4. Present QC stats for input sequences before and after initial pre-processing with ([`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\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nid,fasta\nspecies1,species1_proteins.fasta\nspecies2,species2_proteins.fasta\n```\n\nEach row represents a FASTA file of proteins from a single species.\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/proteinannotator \\\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/proteinannotator/usage) and the [parameter documentation](https://nf-co.re/proteinannotator/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/proteinannotator/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/proteinannotator/output).\n\n## Credits\n\nnf-core/proteinannotator was originally written by Olga Botvinnik and Evangelos Karatzas.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n- [Michael L Heuer](https://github.com/heuermh)\n- [Edmund Miller](https://github.com/edmundmiller)\n- [Eric Wei](https://github.com/eweizy)\n- [Martin Beracochea](https://github.com/mberacochea)\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 `#proteinannotator` channel](https://nfcore.slack.com/channels/proteinannotator) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/proteinannotator for your analysis, please cite it using the following doi: [10.5281/zenodo.18547735](https://doi.org/10.5281/zenodo.18547735)\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": "#aff5d966-2a2a-4cbf-bf15-44cdd5058ceb"
+ "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2"
}
],
"name": "nf-core/proteinannotator"
@@ -132,7 +132,7 @@
}
],
"dateCreated": "",
- "dateModified": "2026-02-09T10:42:29Z",
+ "dateModified": "2026-02-04T13:01:04Z",
"dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
"keywords": [
"nf-core",
@@ -159,10 +159,10 @@
},
"url": [
"https://github.com/nf-core/proteinannotator",
- "https://nf-co.re/proteinannotator/1.0.0/"
+ "https://nf-co.re/proteinannotator/dev/"
],
"version": [
- "1.0.0"
+ "1.1.0dev"
]
},
{
@@ -178,11 +178,11 @@
"version": "!>=25.10.0"
},
{
- "@id": "#aff5d966-2a2a-4cbf-bf15-44cdd5058ceb",
+ "@id": "#fd91eb9d-1f99-4b3e-93f2-56d5b754e7a2",
"@type": "TestSuite",
"instance": [
{
- "@id": "#5d20d507-f40f-4fcc-854d-5d27a47f2941"
+ "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b"
}
],
"mainEntity": {
@@ -191,7 +191,7 @@
"name": "Test suite for nf-core/proteinannotator"
},
{
- "@id": "#5d20d507-f40f-4fcc-854d-5d27a47f2941",
+ "@id": "#fa5732e5-538b-4606-9ac9-3caf643d317b",
"@type": "TestInstance",
"name": "GitHub Actions workflow for testing nf-core/proteinannotator",
"resource": "repos/nf-core/proteinannotator/actions/workflows/nf-test.yml",
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index ac75f97..527d241 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -43,7 +43,7 @@
"untar": 1.34
},
"Workflow": {
- "nf-core/proteinannotator": "v1.0.0"
+ "nf-core/proteinannotator": "v1.1.0dev"
}
},
[
![\"nf-core/proteinannotator\"](\"docs/images/nf-core-proteinannotator_logo_dark.png\"){kind=logo}
\n ![\"nf-core/proteinannotator\"](\"docs/images/proteinannotator_metromap_dark.png\")
\n