full test correct input samplesheet path, typos fix, zenodo doi added to nextflow.config

Author: vagkaratzas

CHANGELOG.md

@@ -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.

conf/test_full.config

@@ -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'

docs/usage.md

@@ -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]'

nextflow.config

@@ -287,7 +287,7 @@ manifest {
     defaultBranch   = 'master'
     nextflowVersion = '!>=25.10.0'
     version         = '1.1.0dev'
-    doi             = ''
+    doi             = '10.5281/zenodo.18547735'
 }
 
 // Nextflow plugins