Add nf-core/eager style ancient DNA (aDNA) analysis workflow

workflows/paleogenomics/adna-analysis/.dockstore.yml

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+version: 1.2
+workflows:
+- name: adna-analysis
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /adna-analysis.ga
+  testParameterFiles:
+  - /adna-analysis-tests.yml
+  authors:
+  - name: Ali Mert AYDIN
+    orcid: "https://orcid.org/0009-0008-9038-0815"

workflows/paleogenomics/adna-analysis/CHANGELOG.md

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+# Changelog
+
+## [0.1] - 2026-05-18
+
+- First release.

workflows/paleogenomics/adna-analysis/README.md

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+# Ancient DNA analysis pipeline
+This workflow performs an ancient DNA (aDNA) based analysis similar to the one in the [nf-core/eager](https://nf-co.re/eager/2.5.3/) workflow. nf-core/eager is a bioinformatics best-practice processing pipeline for genomic NGS sequencing data, with a focus on ancient DNA data. It is ideal for the (palaeo)genomic analysis of humans, animals, plants, microbes and even microbiomes.
+
+The pipeline processes the sequencing-read input provided to the workflow together with a reference genome and optional supporting reference data. It aligns reads and performs extensive general NGS and aDNA-specific quality control on the results.
+
+
+## Required & Optional Inputs
+To run this workflow successfully, you need to provide the following input datasets and parameters:
+
+* **`Choose Read Type` :** Select whether your input is Single-End or Paired-End.
+* **`Input Single-end reads` :** Input single-end FASTQ reads (list collection) for the sample.
+* **`Input Paired-end Forward reads (R1)` :** Input paired-end forward FASTQ reads (list collection) for the sample.
+* **`Input Paired-end reverse reads (R2)` :** Input paired-end reverse FASTQ reads (list collection) for the sample.
+* **`Reference genome` :** Reference genome sequence in FASTA format. This is essential for read mapping and variant calling.
+* **`Choose Mapper` :** Switch to select the alignment tool. Choose between BWA and Bowtie2.
+* **`HapMap chromosome X reference` :** Optional HapMap dataset used for X-chromosome contamination estimation in ANGSD (used only if provided).
+* **`Input Mitochondrial Chromosome Name` :** The exact header name of the mitochondrial chromosome in your reference FASTA file (e.g., MT, chrM, rCRS).
+* **`Kraken2 database directory` :** The database directory required for Kraken2 taxonomic classification.
+* **`Optional BED file for Sex.DetERRmine` :** An optional BED file containing specific genomic coordinates to restrict the Sex.DetERRmine analysis. Leave empty for standard whole-genome human analysis, or provide targeted regions to enable gender estimation for non-human organisms.
+* **`ANGSD region parameter` :** The specific genomic region to restrict the ANGSD analysis (e.g. 'X:5000000-154900000' for human male nuclear contamination estimation; adjust for your reference).
+
+
+## Workflow Steps
+By default the pipeline currently performs the following:
+
+## 1. Preprocessing and Quality Control
+* **Quality Control:** Evaluates read quality before and after trimming (`FastQC`)
+* **Adapter Trimming:** Removes adapter sequences (`AdapterRemoval`)
+
+## 2. Read Mapping and Processing
+* **Alignment:** Maps reads to the provided reference genome conditionally using either (`BWA`) or (`Bowtie2`) based on user selection
+* **Filtering and Statistics:** Separates unmapped reads and calculates alignment statistics (`Samtools View and Flagstat`)
+* **Duplicate Removal:** Detects and marks PCR duplicates (`Picard MarkDuplicates`)
+* **Alignment Quality:** Generates detailed BAM quality metrics (`QualiMap BamQC`)
+* **Library Complexity:** Estimates library complexity (`Preseq`)
+
+## 3. Ancient DNA (aDNA) Analysis
+* **Damage Profiling:** Visualizes aDNA-specific C-to-T damage patterns (`mapDamage`)
+* **Endogenous Content:** Calculates the proportion of endogenous (target) DNA in the sample (`EndorSpy`)
+* **(`Optional`) Contamination:** Estimates nuclear X-chromosome contamination conditionally if HapMap data is provided (`ANGSD X-Contamination`)
+
+## 4. Biological Information
+* **Sex Determination:** Determines biological sex based on relative chromosome coverage ratio. This step adapts conditionally whether an optional BED file is provided (`Sex.DetERRmine`)
+* **Mt/Nuc Ratio:** Calculates the ratio of mitochondrial reads to nuclear reads utilizing the specified mitochondrial chromosome name (`MtNucRatioCalculator`)
+
+## 5. Genotyping
+* **Variant Analysis:** Performs variant calling to generate VCF files (`FreeBayes`)
+* **Variant Statistics:** Calculates statistics for the generated variants (`Bcftools stats`)
+
+## 6. Metagenomic Screening (For Unmapped Reads)
+* **Read Extraction:** Extracts unmapped reads for microbial analysis (`Picard SamToFastq`)
+* **Quality Filter:** Filters low-complexity sequences (`BBTools BBduk`)
+* **Taxonomic Classification:** Performs microbiome/taxonomic screening on the filtered unmapped reads (`Kraken2`)
+
+## 7. Reporting
+* **Summary Report:** Aggregates logs and statistics from all these tools into a single interactive HTML report (`MultiQC`)
+
+
+## Workflow Outputs
+Upon successful execution, the workflow explicitly provides the following final files for analysis:
+
+* **`MultiQC aggregated workflow summary report` :** An interactive HTML report aggregating QC and analysis logs from all tools.
+* **`QualiMap BamQC general alignment quality metrics report` :** A detailed HTML report containing mapping quality metrics, GC content, and coverage statistics.
+* **`mapDamage Visualisation` :** Visual plots displaying the characteristic C-to-T deamination patterns at the ends of ancient DNA reads.
+* **`Kraken2 taxonomic classification and microbial screening report` :** A tabular report showing the taxonomic classification of unmapped reads.
+* **`EndorSpy endogenous DNA authentication report` :** A JSON file containing the calculated endogenous DNA percentage.
+* **`Sex.DetERRmine (Without BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for human-genome alignments.
+* **`Sex.DetERRmine (With BED) report of chromosomal gender estimation` :** A JSON file containing biological sex metrics for targeted capture regions.
+* **`Mitochondrial to nuclear DNA ratio calculation report` :** A JSON file containing the calculated ratio between mitochondrial and nuclear reads.
+* **`ANGSD report of nuclear contamination estimation` :** A tabular text file detailing the estimates of nuclear X-chromosome contamination.
+* **`Bcftools variant calling summary statistics report` :** A text file containing comprehensive summary statistics for the called variants (VCF).
+* **`Fully post-processed mapping results` :** The final deduplicated and filtered alignment BAM file.
+* **`FreeBayes raw genomic variant calls` :** The raw VCF file generated from variant analysis.
+
+
+## Testing Data
+To ensure the workflow functions correctly, it was validated using the following datasets and databases:
+
+* **`Primary Test Data` :** A downsampled paired-end FASTQ dataset [NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz) and [NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz](https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz) optimized for rapid workflow testing and validation.
+* **`Primary Reference Genome` :** The [hs37d5_chr21-MT.fa.gz](https://github.com/nf-core/test-datasets/blob/eager/reference/Human/hs37d5_chr21-MT.fa.gz) file was utilized as the primary reference genome sequence.
+* **`X-Chromosome Contamination Reference` :** The [HapMap ChrX](https://github.com/ANGSD/angsd/blob/master/RES/HapMapChrX.gz) dataset was provided as the initial reference for the estimation of X-chromosome contamination using the ANGSD tool.
+* **`Taxonomic Classification Database` :** The Minikraken v2 database was utilized to perform taxonomic classification via Kraken2.

workflows/paleogenomics/adna-analysis/adna-analysis-tests.yml

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+- doc: Test outline for adna-analysis.ga (Single-End, BWA, No BED, HapMap Present)
+  job:
+    Choose Read Type: Single-End
+    Input Single-end reads:
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: NIST7035
+        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
+        filetype: fastqsanger.gz
+    Reference genome:
+      class: File
+      location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz
+      filetype: fasta.gz
+    HapMap chromosome X reference:
+      class: File
+      location: https://github.com/ANGSD/angsd/raw/master/RES/HapMapChrX.gz
+      filetype: gz
+    Choose Mapper: BWA
+    Optional BED file for Sex.DetERRmine: null
+    Kraken2 database directory: viral2019-03
+  outputs:
+    Fully post-processed mapping results:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_size:
+              min: 100
+    EndorSpy endogenous DNA authentication report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "percent_on_target"
+    Sex.DetERRmine (Without BED) report of chromosomal gender estimation:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "Sex.DetERRmine"
+    QualiMap BamQC general alignment quality metrics report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "Qualimap Report: BAM QC"
+    Mitochondrial to nuclear DNA ratio calculation report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "mtnuccalculator"
+    mapDamage Visualisation:
+      element_tests:
+        NIST7035:
+          element_tests:
+            dnacomp:
+              asserts:
+                has_text:
+                  text: "mapDamage"
+    FreeBayes raw genomic variant calls:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "freeBayes"
+    ANGSD report of nuclear contamination estimation:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "Method1_MOM_estimate"
+    Bcftools variant calling summary statistics report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "ACT>TCGA"
+    Kraken2 taxonomic classification and microbial screening report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "root"
+    MultiQC aggregated workflow summary report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "MultiQC"
+
+- doc: Test outline for adna-analysis.ga (Paired-End, Bowtie2, BED Present, No HapMap)
+  job:
+    Choose Read Type: Paired-End
+    Input Paired-end Forward reads (R1):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: NIST7035
+        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R1_001_10MB.fastq.gz
+        filetype: fastqsanger.gz
+    Input Paired-end reverse reads (R2):
+      class: Collection
+      collection_type: list
+      elements:
+      - class: File
+        identifier: NIST7035
+        location: https://zenodo.org/records/21222737/files/NIST7035_TAAGGCGA_L001_R2_001_10MB.fastq.gz
+        filetype: fastqsanger.gz
+    Reference genome:
+      class: File
+      location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/hs37d5_chr21-MT.fa.gz
+      filetype: fasta.gz
+    HapMap chromosome X reference: null
+    Choose Mapper: Bowtie2
+    Optional BED file for Sex.DetERRmine:
+      class: File
+      location: https://github.com/nf-core/test-datasets/raw/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz
+      filetype: tabular
+    Kraken2 database directory: viral2019-03
+  outputs:
+    Fully post-processed mapping results:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_size:
+              min: 100
+    EndorSpy endogenous DNA authentication report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "percent_on_target"
+    Sex.DetERRmine (With BED) report of chromosomal gender estimation:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "Sex.DetERRmine"
+    QualiMap BamQC general alignment quality metrics report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "Qualimap Report: BAM QC"
+    Mitochondrial to nuclear DNA ratio calculation report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "mtnuccalculator"
+    mapDamage Visualisation:
+      element_tests:
+        NIST7035:
+          element_tests:
+            dnacomp:
+              asserts:
+                has_text:
+                  text: "mapDamage"
+    FreeBayes raw genomic variant calls:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "freeBayes"
+    Bcftools variant calling summary statistics report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "ACT>TCGA"
+    Kraken2 taxonomic classification and microbial screening report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "root"
+    MultiQC aggregated workflow summary report:
+      element_tests:
+        NIST7035:
+          asserts:
+            has_text:
+              text: "MultiQC"