citations, output.md and reference bibliography texts updated

Author: vagkaratzas

CHANGELOG.md

@@ -14,7 +14,7 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 - [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing
 - [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1
 - [#47](https://github.com/nf-core/proteinannotator/pull/47) - Update metromap with more tools added from [May 2025 Hackathon](https://nf-co.re/events/2025/hackathon-boston)
-- [#43](https://github.com/nf-core/proteinannotator/pull/44) - Add [mTM-Align](https://nf-co.re/modules/mtmalign_align/) and [MMseqs2 Search](https://nf-co.re/modules/mmseqs_search/) modules
+<!-- - [#43](https://github.com/nf-core/proteinannotator/pull/44) - Add [mTM-Align](https://nf-co.re/modules/mtmalign_align/) and [MMseqs2 Search](https://nf-co.re/modules/mmseqs_search/) modules -->
 - [#42](https://github.com/nf-core/proteinannotator/pull/42) - Updated to `nf-test` on GitHub Actions and in the `PULL_REQUEST_TEMPLATE.md`
 - [#13](https://github.com/nf-core/proteinannotator/pull/13) - Add nf-core seqkit/stats module
 - [#9](https://github.com/nf-core/proteinannotator/pull/9) - Add [InterProScan](https://interproscan-docs.readthedocs.io/) module

CITATIONS.md

@@ -10,21 +10,29 @@
 
 ## Pipeline tools
 
-- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+- [SeqFu](https://pubmed.ncbi.nlm.nih.gov/34066939/)
 
-> 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.
+> Telatin A, Fariselli P, Birolo G. SeqFu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering. 2021 May 7;8(5):59. doi: 10.3390/bioengineering8050059. PubMed PMID: 34066939; PubMed Central PMCID: PMC8148589.
+
+- [SeqKit](https://pubmed.ncbi.nlm.nih.gov/38898985/)
+
+> Shen W, Sipos B, Zhao L. SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. 2024 Apr 5:e191. doi: 10.1002/imt2.191. PubMed PMID: 38898985; PubMed Central PMCID: PMC11183193.
 
 - [InterProScan](https://academic.oup.com/bioinformatics/article/17/9/847/206564)
 
 > Zdobnov, Evgeni M., and Rolf Apweiler. “InterProScan – an Integration Platform for the Signature-Recognition Methods in InterPro.” Bioinformatics 17, no. 9 (September 1, 2001): 847–48. https://doi.org/10.1093/bioinformatics/17.9.847.
 
-- [MMseqs2](https://www.nature.com/articles/nbt.3988)
+<!-- - [MMseqs2](https://www.nature.com/articles/nbt.3988)
 
 > Zdobnov, Evgeni M., and Rolf Apweiler. “InterProScan – an Integration Platform for the Signature-Recognition Methods in InterPro.” Bioinformatics 17, no. 9 (September 1, 2001): 847–48. https://doi.org/10.1093/bioinformatics/17.9.847.
 
 - [mTM-align](https://academic.oup.com/bioinformatics/article/34/10/1719/4769500)
 
-> Dong, Runze, Zhenling Peng, Yang Zhang, and Jianyi Yang. “mTM-Align: An Algorithm for Fast and Accurate Multiple Protein Structure Alignment.” Bioinformatics 34, no. 10 (May 15, 2018): 1719–25. https://doi.org/10.1093/bioinformatics/btx828.
+> Dong, Runze, Zhenling Peng, Yang Zhang, and Jianyi Yang. “mTM-Align: An Algorithm for Fast and Accurate Multiple Protein Structure Alignment.” Bioinformatics 34, no. 10 (May 15, 2018): 1719–25. https://doi.org/10.1093/bioinformatics/btx828. -->
+
+- [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.
 
 ## Software packaging/containerisation tools
 

assets/methods_description_template.yml

@@ -3,7 +3,6 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/proteinannotator Methods Description"
 section_href: "https://github.com/nf-core/proteinannotator"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>

docs/output.md

@@ -12,12 +12,51 @@ 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:
 
+- [Quality check and preprocessing](#quality-check-and-preprocessing)
+  - [SeqFu](#seqfu) for input amino acid sequences quality check (QC)
+  - [SeqKit](#seqkit) for preprocessing input amino acid sequences (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences)
+
 - [Functional Annotation](#functional-annotation) Annotate proteins with functional domains
   - [InterProScan](#Interproscan) - Search the InterPro database for functional domains
 - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
-- [SeqKit stats](#seqkit_stats) - Simple statistics for protein FASTA files
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
+### Quality check and preprocessing
+
+#### SeqFu
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `qc/`
+  - `<samplename>/`
+    - `<samplename>_before.tsv`: Statistics for the input amino acid sequences before preprocessing
+    - `<samplename>_before_mqc.txt`: Statistics for the input amino acid sequences in MultiQC-ready format before preprocessing
+    - `<samplename>_after.tsv`: (optional) Statistics for the input amino acid sequences after preprocessing
+    - `<samplename>_after_mqc.txt`: (optional) Statistics for the input amino acid sequences in MultiQC-ready format after preprocessing
+    - `<samplename>.log`: (optional) Output file with count of duplicate sequences that were found and removed
+
+</details>
+
+The `seqfu` module is used for statistics generation of input amino acid sequences, both before and after preprocessing.
+
+[SeqFu](https://github.com/telatin/seqfu2) is a cross-platform compiled suite of tools to manipulate and inspect `FASTA` and `FASTQ` files.
+
+#### SeqKit
+
+<details markdown="1">
+<summary>Output files</summary>
+
+- `qc/`
+  - `<samplename>/`
+    - `<samplename>.<suffix>`: Updated preprocessed input fasta file
+
+</details>
+
+The `seqkit` module is used for initial preprocessing (i.e., gap removal, convert to upper case, validate, filter by length, replace special characters such as `/`, and remove duplicate sequences) of the input amino acid sequences.
+
+[SeqKit](https://github.com/shenwei356/seqkit) is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
+
 ### Functional Annotation
 
 #### InterProScan

subworkflows/local/utils_nfcore_proteinannotator_pipeline/main.nf

@@ -174,30 +174,33 @@ def validateInputSamplesheet(input) {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
+
+    def quality_check_text = [
+        "Amino acid sequence statistics were generated with SeqFu (Telatin et al. 2021).",
+        params.skip_preprocessing ? "" : "Input sequences were preprocessed with SeqKit (gap trimming, length filtering, validation, duplicate removal) (Shen et al. 2024)."
+    ].join(' ').trim()
+
+    def postprocessing_text = "Run statistics were reported using MultiQC (Ewels et al. 2016)."
+
     def citation_text = [
-        "Tools used in the workflow included:",
-        "Nextflow (Di Tommaso et al. 2017),",
-        "nf-core (Ewels et al. 2020),",
-        "Bioconda (Grüning et al. 2018),",
-        "BioContainers (da Veiga Leprevost et al. 2017),",
-        "MultiQC (Ewels et al. 2016),",
-        "SeqKit (Shen 2016),",
-        "Anaconda (Anaconda Software Distribution 2016),",
-        "Docker (Merkel 2014),",
-        "Singularity (Kurtzer et al. 2017)",
-        ".",
+        quality_check_text,
+        postprocessing_text
     ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
+    def quality_check_text = [
+        '<li>Telatin, A., Fariselli, P., & Birolo, G. (2021). SeqFu: a suite of utilities for the robust and reproducible manipulation of sequence files. Bioengineering, 8(5), 59. doi: <a href="https://doi.org/10.3390/bioengineering8050059">10.3390/bioengineering8050059</a></li>',
+        params.skip_preprocessing ? '' : '<li>Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss army knife for sequence and alignment processing. Imeta, 3(3), e191. doi: <a href="https://doi.org/10.1002/imt2.191">10.1002/imt2.191</a></li>'
+    ].join(' ').trim()
+
+    def postprocessing_text = '<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047–3048. doi: <a href="https://doi.org/10.1093/bioinformatics/btw354">10.1093/bioinformatics/btw354</a></li>'
+
     def reference_text = [
-        "<li>Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. doi: /10.1093/bioinformatics/btw354</li>",
-        "<li>Shen W, Le S, Li Y, Hu F (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962. doi: https://doi.org/10.1371/journal.pone.0163962</li>",
-        "<li>Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.</li>",
-        "<li>Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: https://10.5555/2600239.2600241.</li>",
-        "<li>Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: https://10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.</li>",
+        quality_check_text,
+        postprocessing_text
     ].join(' ').trim()
 
     return reference_text

workflows/proteinannotator.nf

@@ -40,7 +40,7 @@ workflow PROTEINANNOTATOR {
             meta, _fasta, updated_fasta ->
             [ meta, updated_fasta ]
         }
-    ch_samplesheet_updated.view()
+
     FUNCTIONAL_ANNOTATION( ch_samplesheet_updated )
     ch_versions = ch_versions.mix( FUNCTIONAL_ANNOTATION.out.versions.first() )