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vagkaratzas merged 1 commit into from
Mar 12, 2026
Merged

full test correct input samplesheet path, typos fix, zenodo doi added… #85

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8 changes: 8 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## v1.1.0dev - [date]

### `Added`

- [85](https://github.com/nf-core/proteinannotator/pull/85) - Added zenodo doi in `nextflow.config`. (by @vagkaratzas)

### `Changed`

- [85](https://github.com/nf-core/proteinannotator/pull/85) - `test_full.config` input samplesheet path is now set properly. (by @vagkaratzas)

## v1.0.0 - Yellow Saiga - [2026/02/09]

Initial release of nf-core/proteinannotator, created with the [nf-core](https://nf-co.re/) template.
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2 changes: 1 addition & 1 deletion conf/test_full.config
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Expand Up @@ -15,7 +15,7 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = params.pipelines_testdata_base_path + 'proteinannotator/testdata/samplesheet.csv'
input = params.pipelines_testdata_base_path + 'proteinannotator/samplesheet/samplesheet.csv'
// Domain annotation
pfam_latest_link = params.pipelines_testdata_base_path + 'proteinannotator/testdata/pfam/Pfam-A_test.hmm.gz'
funfam_latest_link = params.pipelines_testdata_base_path + 'proteinannotator/testdata/funfam/funfam-hmm3-v4_3_0_test.lib.gz'
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6 changes: 4 additions & 2 deletions docs/usage.md
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Expand Up @@ -6,11 +6,13 @@

## 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. -->
**nf-core/proteinannotator** is a bioinformatics pipeline that computes statistics and generates sequence-level annotations for amino acid sequences.
It takes a protein FASTA file as input and performs conserved domain annotation (using Pfam and FunFam HMM databases), functional annotation (using InterProScan), and secondary structure prediction (using s4pred).
Optionally, paths to pre-downloaded databases can be provided to skip the automatic download steps and speed up repeated runs.

## 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.
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 2 columns, and a header row as shown in the examples below.

```bash
--input '[path to samplesheet file]'
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -287,7 +287,7 @@ manifest {
defaultBranch = 'master'
nextflowVersion = '!>=25.10.0'
version = '1.1.0dev'
doi = ''
doi = '10.5281/zenodo.18547735'
}

// Nextflow plugins
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