Merge branch 'dev' into nf-core-template-merge-3.1.0

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js}]
+[*.{md,yml,yaml,html,css,scss,js,cff}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/workflows/ci.yml

@@ -43,6 +43,15 @@ jobs:
             profile: "conda"
           - isMaster: false
             profile: "singularity"
+        PARAMS:
+          - " --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
+          - " --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
+          - " --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
+          - " --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
+          - " --mapping_tool circularmapper --skip_preprocessing --convert_inputbam --fasta_circular_target 'NC_007596.2' --fasta_circularmapper_elongationfactor 500"
+          - "_humanbam --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
+          - "_humanbam --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
+          - "_multiref" ## TODO add damage manipulation here instead once it goes multiref
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
@@ -82,4 +91,4 @@ jobs:
 
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{matrix.profile}},${{ matrix.test_name }}${{ matrix.PARAMS }} --outdir ./results

.gitignore

@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.nf-test*

.prettierignore

@@ -10,3 +10,6 @@ testing/
 testing*
 *.pyc
 bin/
+*.cff
+test/
+dev_docs.md

CITATION.cff

@@ -0,0 +1,52 @@
+cff-version: 1.2.0
+message: "If you use `nf-core/eager` in your work, please cite the following publication"
+authors:
+  - family-names: Fellows Yates
+    given-names: James A.
+  - family-names: Lamnidis
+    given-names: Thiseas C.
+  - family-names: Borry
+    given-names: Maxime
+  - family-names: Andrades Valtueña
+    given-names: Aida
+  - family-names: Fagernãs
+    given-names: Zandra
+  - family-names: Clayton
+    given-names: Stephen
+  - family-names: Garcia
+    given-names: Maxime U.
+  - family-names: Neukamm
+    given-names: Judith
+  - family-names: Peltzer
+    given-names: Alexander
+title: "Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager"
+version: 3.0.0
+doi: 10.7717/peerj.10947
+date-released: 2022-08-02
+url: https://github.com/nf-core/eager
+prefered-citation:
+  type: article
+  authors:
+    - family-names: Fellows Yates
+      given-names: James A.
+    - family-names: Lamnidis
+      given-names: Thiseas C.
+    - family-names: Borry
+      given-names: Maxime
+    - family-names: Andrades Valtueña
+      given-names: Aida
+    - family-names: Fagernãs
+      given-names: Zandra
+    - family-names: Clayton
+      given-names: Stephen
+    - family-names: Garcia
+      given-names: Maxime U.
+    - family-names: Neukamm
+      given-names: Judith
+    - family-names: Peltzer
+      given-names: Alexander
+  doi: 10.7717/peerj.10947
+  start: e10947
+  title: "Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager"
+  year: 2021
+  url: https://dx.doi.org/10.1038/10.7717/peerj.10947

README.md

@@ -1,7 +1,7 @@
 <h1>
   <picture>
-    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-eager_logo_dark.png">
-    <img alt="nf-core/eager" src="docs/images/nf-core-eager_logo_light.png">
+    <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core_eager_logo_outline_drop.png">
+    <img alt="nf-core/eager" src="docs/images/nf-core_eager_logo_outline_drop.png">
   </picture>
 </h1>
 
@@ -19,50 +19,99 @@
 
 ## Introduction
 
-**nf-core/eager** is a bioinformatics pipeline that ...
+**nf-core/eager** is a scalable and reproducible bioinformatics best-practise processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA (aDNA) data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.
 
-<!-- TODO nf-core:
-   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
-   major pipeline sections and the types of output it produces. You're giving an overview to someone new
-   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
--->
+## Pipeline summary
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
 <!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
 
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+- (Optionally) create reference genome indices for mapping (`bwa`, `samtools`, and `picard`)
+- Sequencing quality control (`FastQC`, `Falco`)
+- Sequencing adapter removal, paired-end data merging (`AdapterRemoval`)
+- Read mapping to reference using (`bwa aln`, `bwa mem`, `CircularMapper`, or `bowtie2`)
+- Post-mapping processing, statistics and conversion to bam (`samtools`, and `preseq`)
+- Ancient DNA C-to-T damage pattern visualisation (`DamageProfiler`)
+- PCR duplicate removal (`DeDup` or `MarkDuplicates`)
+- Post-mapping statistics and BAM quality control (`Qualimap`)
+- Library Complexity Estimation (`preseq`)
+- Overall pipeline statistics summaries (`MultiQC`)
+
+### Additional Steps
+
+Additional functionality contained by the pipeline currently includes:
+
+#### Input
+
+- Automatic merging of complex sequencing setups (e.g. multiple lanes, sequencing configurations, library types)
+
+#### Preprocessing
+
+- Illumina two-coloured sequencer poly-G tail removal (`fastp`)
+- Post-AdapterRemoval trimming of FASTQ files prior mapping (`fastp`)
+- Automatic conversion of unmapped reads to FASTQ (`samtools`)
+- Host DNA (mapped reads) stripping from input FASTQ files (for sensitive samples)
+
+#### aDNA Damage manipulation
+
+- Damage removal/clipping for UDG+/UDG-half treatment protocols (`BamUtil`)
+- Damaged reads extraction and assessment (`PMDTools`)
+- Nuclear DNA contamination estimation of human samples (`angsd`)
+
+#### Genotyping
+
+- Creation of VCF genotyping files (`GATK UnifiedGenotyper`, `GATK HaplotypeCaller` and `FreeBayes`)
+- Creation of EIGENSTRAT genotyping files (`pileupCaller`)
+- Creation of Genotype Likelihood files (`angsd`)
+- Consensus sequence FASTA creation (`VCF2Genome`)
+- SNP Table generation (`MultiVCFAnalyzer`)
+
+#### Biological Information
+
+- Mitochondrial to Nuclear read ratio calculation (`MtNucRatioCalculator`)
+- Statistical sex determination of human individuals (`Sex.DetERRmine`)
+
+#### Metagenomic Screening
+
+- Low-sequenced complexity filtering (`BBduk` or `PRINSEQ++`)
+- Taxonomic binner with alignment (`MALT` or `MetaPhlAn 4`)
+- Taxonomic binner without alignment (`Kraken2`,`KrakenUniq`)
+- aDNA characteristic screening of taxonomically binned data from MALT (`MaltExtract`)
+
+#### Functionality Overview
+
+A graphical overview of suggested routes through the pipeline depending on context can be seen below.
+
+<p align="center">
+    <img src="docs/images/eager2_metromap_complex.png" alt="nf-core/eager metro map" width="70%"
+</p>
 
 ## Usage
 
 > [!NOTE]
 > 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.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.csv`:
+`samplesheet.tsv`:
 
 ```csv
-sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+ample_id	library_id	lane	colour_chemistry	pairment	strandedness	damage_treatment	r1	r2	bam	bam_reference_id
+sample1	sample1_a	1	4	paired	double	none	/<path>/<to>/sample1_a_l1_r1.fq.gz /<path>/<to>/sample1_a_l1_r2.fq.gz	NA	NA
+sample2	sample2_a	2	2	single	double	full	/<path>/<to>/sample2_a_l1_r1.fq.gz	NA	NA	NA
+sample3	sample3_a	8	4	single	double	half	NA	NA	/<path>/<to>/sample31_a.bam	Mammoth_MT_Krause
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
+Each row represents a fastq file (single-end), pair of fastq files (paired end), and/or a bam file.
 
 Now, you can run the pipeline using:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run nf-core/eager \
    -profile <docker/singularity/.../institute> \
    --input samplesheet.csv \
+   --fasta  '<your_reference>.fasta' \
    --outdir <OUTDIR>
 ```
 
@@ -79,11 +128,40 @@ For more details about the output files and reports, please refer to the
 
 ## Credits
 
-nf-core/eager was originally written by The nf-core/eager community.
+This pipeline was established by Alexander Peltzer ([apeltzer](https://github.com/apeltzer)) and [James A. Fellows Yates](https://github.com/jfy133). Version two had major contributions from [Stephen Clayton](https://github.com/sc13-bioinf), [Thiseas C. Lamnidis](https://github.com/TCLamnidis), [Maxime Borry](https://github.com/maxibor), [Zandra Fagernäs](https://github.com/ZandraFagernas), [Aida Andrades Valtueña](https://github.com/aidaanva) and [Maxime Garcia](https://github.com/MaxUlysse) and the nf-core community.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
-<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+- [Alex Hübner](https://github.com/alexhbnr)
+- [Alexandre Gilardet](https://github.com/alexandregilardet)
+- Arielle Munters
+- [Åshild Vågene](https://github.com/ashildv)
+- [Charles Plessy](https://github.com/charles-plessy)
+- [Elina Salmela](https://github.com/esalmela)
+- [Fabian Lehmann](https://github.com/Lehmann-Fabian)
+- [He Yu](https://github.com/paulayu)
+- [Hester van Schalkwyk](https://github.com/hesterjvs)
+- [Ian Light-Máka](https://github.com/ilight1542)
+- [Ido Bar](https://github.com/IdoBar)
+- [Irina Velsko](https://github.com/ivelsko)
+- [Işın Altınkaya](https://github.com/isinaltinkaya)
+- [Johan Nylander](https://github.com/nylander)
+- [Jonas Niemann](https://github.com/NiemannJ)
+- [Katerine Eaton](https://github.com/ktmeaton)
+- [Kathrin Nägele](https://github.com/KathrinNaegele)
+- [Kevin Lord](https://github.com/lordkev)
+- [Luc Venturini](https://github.com/lucventurini)
+- [Mahesh Binzer-Panchal](https://github.com/mahesh-panchal)
+- [Marcel Keller](https://github.com/marcel-keller)
+- [Megan Michel](https://github.com/meganemichel)
+- [Merlin Szymanski](https://github.com/merszym)
+- [Pierre Lindenbaum](https://github.com/lindenb)
+- [Pontus Skoglund](https://github.com/pontussk)
+- [Raphael Eisenhofer](https://github.com/EisenRa)
+- [Roberta Davidson](https://github.com/roberta-davidson)
+- [Rodrigo Barquera](https://github.com/RodrigoBarquera)
+- [Selina Carlhoff](https://github.com/scarlhoff)
+- [Torsten Günter](https://bitbucket.org/tguenther)
 
 ## Contributions and Support
 
@@ -93,10 +171,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/eager for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+If you use nf-core/eager for your analysis, please cite it using the following doi:
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+> Fellows Yates JA, Lamnidis TC, Borry M, Valtueña Andrades A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. 2021. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 9:e10947. DOI: [10.7717/peerj.10947](https://doi.org/10.7717/peerj.10947).
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.