Check guidelines for release and add corrections (nf-core#132)

* typo fixes in readme

* remove some to-dos

* remove todos, add bibliography

* add conditional detection of tools

* add missing tools to citations

* add conditional params

* add release name and date

* bump versions

* add contributors and reviewers

* Update README.md

* Update README.md

* Update README.md

---------

Co-authored-by: Louis LE NEZET <[email protected]>

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v1.0dev - [date]
+## v1.0.0 - Black Labrador [2024-10-28]
 
 Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co.re/) template.
 
@@ -69,3 +69,12 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 ### `Dependencies`
 
 ### `Deprecated`
+
+### `Contributors`
+
+[Louis Le Nezet](https://github.com/LouisLeNezet)
+[Anabella Trigila](https://github.com/atrigila)
+[Eugenia Fontecha](https://github.com/eugeniafontecha)
+[Maxime U Garcia](https://github.com/maxulysse)
+[Matias Romero Victorica](https://github.com/mrvictorica)
+[Nicolas Schcolnicov](https://github.com/nschcolnicov)

CITATIONS.md

@@ -18,6 +18,14 @@
 
 > Rubinacci, S., Ribeiro, D. M., Hofmeister, R. J., & Delaneau, O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics, 53(1), 120-126.
 
+- [GLIMPSE2](https://doi.org/10.1038/s41588-023-01438-3)
+
+> Rubinacci, S., Hofmeister, R. J., Sousa da Mota, B., & Delaneau, O. (2023). Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. Nature genetics 55, 1088–1090.
+
+- [STITCH](https://doi.org/10.1038/ng.3594)
+
+> Davies, R. W., Flint, J., Myers, S., & Mott, R.(2016). Rapid genotype imputation from sequence without reference panels. Nature genetics 48, 965–969.
+
 - [Shapeit](https://odelaneau.github.io/shapeit5/)
 
 > Hofmeister RJ, Ribeiro DM, Rubinacci S., Delaneau O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nature Genetics doi: https://doi.org/10.1038/s41588-023-01415-w

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/phaseimpute/tree/dev" target="_blank">nf-core/phaseimpute</a>
+  This report has been generated by the <a href="https://github.com/nf-core/phaseimpute/releases/tag/1.0.0" target="_blank">nf-core/phaseimpute</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/phaseimpute/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/phaseimpute/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-phaseimpute-methods-description":
     order: -1000

conf/base.config

@@ -10,7 +10,6 @@
 
 process {
 
-    // TODO nf-core: Check the defaults for all processes
     cpus   = { 1      * task.attempt }
     memory = { 6.GB   * task.attempt }
     time   = { 4.h    * task.attempt }
@@ -24,7 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { 1                   }

docs/development.md

@@ -1,5 +1,9 @@
 # Development
 
+## Style
+
+Names of releases are composed of a color + a dog breed.
+
 ## Features and tasks
 
 - [x] Add automatic detection of chromosome name to create a renaming file for the vcf files

docs/output.md

@@ -6,8 +6,6 @@ This document describes the output produced by the pipeline. Most of the plots a
 
 The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory.
 
-<!-- TODO nf-core: Write this documentation describing your workflow's output -->
-
 ## Pipeline overview
 
 ## Panel preparation outputs `--steps panelprep`

docs/usage.md

@@ -6,8 +6,6 @@
 
 ## 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. -->
-
 ## 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.

nextflow.config

@@ -216,8 +216,7 @@ profiles {
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
 // Load nf-core/phaseimpute custom profiles from different institutions.
-// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
-// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/phaseimpute.config" : "/dev/null"
+includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/phaseimpute.config" : "/dev/null"
 
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
@@ -280,7 +279,7 @@ manifest {
     description     = """Phasing and imputation pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '1.0dev'
+    version         = '1.0.0'
     doi             = ''
 }
 

subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf

@@ -597,27 +597,40 @@ def genomeExistsError() {
 // Generate methods description for MultiQC
 //
 def toolCitationText() {
-    // TODO nf-core: Optionally add in-text citation tools to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def citation_text = [
-            "Tools used in the workflow included:",
-            "FastQC (Andrews 2010),",
-            "MultiQC (Ewels et al. 2016)",
-            "."
-        ].join(' ').trim()
+        "Tools used in the workflow included:",
+        "BCFtools (Danecek et al. 2021),",
+        params.tools ? params.tools.split(',').contains("glimpse")   ? "GLIMPSE (Rubinacci et al. 2020)," : "" : "",
+        params.tools ? params.tools.split(',').contains("glimpse2")  ? "GLIMPSE2 (Rubinacci et al. 2023)," : "": "",
+        params.tools ? params.tools.split(',').contains("quilt")     ? "QUILT (Davies et al. 2021)," : "": "",
+        "SAMtools (Li et al. 2009),",
+        params.tools ? params.phased ? "SHAPEIT5 (Hofmeister et al. 2023)," : "": "",
+        params.tools ? params.phased ? "BEDtools (Quinlan and Hall 2010)," : "": "",
+        params.tools ? params.tools.split(',').contains("stitch")    ? "STITCH (Davies et al. 2016)," : "": "",
+        "Tabix (Li et al. 2011),",
+        params.tools ? params.compute_freq  ? "VCFlib (Garrison et al. 2022)," : "": "",
+        "."
+    ].join(' ').trim()
 
     return citation_text
 }
 
 def toolBibliographyText() {
-    // TODO nf-core: Optionally add bibliographic entries to this list.
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-            "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).</li>",
-            "<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>"
-        ].join(' ').trim()
+        params.phased ? "<li>Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi:10.1093/bioinformatics/btq033.</li>": "",
+        "<li>Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi:10.1093/bioinformatics/btp352.</li>",
+        "<li>Li H. (2011). Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011 Mar 1;27(5):718-9. doi:10.1093/bioinformatics/btq671.</li>",
+        params.tools ? params.tools.split(',').contains("quilt") ? "<li>Davies RW, Kucka M, Su D, Shi S, Flanagan M, Cunniff CM, Chan YF, & Myers S. (2021). Rapid genotype imputation from sequence with reference panels. Nature Genetics. doi:10.1038/s41588-021-00877-0.</li>" : "": "",
+        params.tools ? params.tools.split(',').contains("glimpse") ? "<li>Rubinacci S, Ribeiro DM, Hofmeister RJ, & Delaneau O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics. doi:10.1038/s41588-020-00756-0.</li>" : "": "",
+        params.tools ? params.tools.split(',').contains("glimpse2") ? "<li>Rubinacci S, Hofmeister RJ, Sousa da Mota B, & Delaneau O. (2023). Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. Nature Genetics. doi:10.1038/s41588-023-01438-3.</li>" : "": "",
+        params.phased ? "<li>Hofmeister RJ, Ribeiro DM, Rubinacci S, Delaneau O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nat Genet. 2023 Jul;55(7):1243-1249. doi:10.1038/s41588-023-01415-w.</li>" : "",
+        params.tools ? params.tools.split(',').contains("stitch") ? "<li>Davies RW, Flint J, Myers S, & Mott R. (2016). Rapid genotype imputation from sequence without reference panels. Nature Genetics.</li>" : "": "",
+        params.compute_freq ? "<li>Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS, Prins P. (2022). A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PLoS Comput Biol 18(5).</li>" : "",
+    ].join(' ').trim()
 
     return reference_text
 }
@@ -646,9 +659,8 @@ def methodsDescriptionText(mqc_methods_yaml) {
     meta["tool_citations"] = ""
     meta["tool_bibliography"] = ""
 
-    // TODO nf-core: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
-    // meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
-    // meta["tool_bibliography"] = toolBibliographyText()
+    meta["tool_citations"] = toolCitationText().replaceAll(", \\.", ".").replaceAll("\\. \\.", ".").replaceAll(", \\.", ".")
+    meta["tool_bibliography"] = toolBibliographyText()
 
 
     def methods_text = mqc_methods_yaml.text