Merge pull request #8 from snakemake-workflows/better-tables

feat: better tables, CI testing, wrapper and env updates, reference cleanup, release-please, conventional commits, CITATION.cff, Zenodo activation

.github/workflows/conventional-prs.yaml

@@ -0,0 +1,18 @@
+name: "Lint PR for conventional commits: https://www.conventionalcommits.org"
+
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  main:
+    name: Validate PR title
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v5
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/main.yaml

@@ -0,0 +1,58 @@
+name: Tests
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches_ignore: []
+
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # Full git history is needed to get a proper
+          # list of changed files within `super-linter`
+          fetch-depth: 0
+      - name: Formatting
+        uses: github/super-linter@v4
+        env:
+          VALIDATE_ALL_CODEBASE: false
+          DEFAULT_BRANCH: main
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          VALIDATE_SNAKEMAKE_SNAKEFMT: true
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Lint workflow
+      uses: snakemake/snakemake-github-action@v1
+      with:
+        directory: .
+        snakefile: workflow/Snakefile
+        stagein: "mamba install -y -n snakemake --channel conda-forge pyarrow=6.0"
+        args: "--lint"
+
+  Testing:
+    runs-on: ubuntu-latest
+    needs: 
+      - Linting
+      - Formatting
+    steps:
+    - uses: actions/checkout@v3
+    - name: Test workflow
+      uses: snakemake/snakemake-github-action@v1
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--configfile .test/config/config.yaml --use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache"
+
+    - name: Test report
+      uses: snakemake/snakemake-github-action@v1
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--configfile .test/config/config.yaml --report report.zip"

.github/workflows/release-please.yaml

@@ -0,0 +1,15 @@
+name: "release-please, see: https://github.com/marketplace/actions/release-please-action"
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: google-github-actions/release-please-action@v3
+        with:
+          release-type: simple
+          token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -0,0 +1,14 @@
+.test/benchmarks/**
+.test/logs/**
+.test/resources/*.fai
+.test/resources/*.gz
+.test/resources/*.mmi
+.test/results/**
+.test/.snakemake/**
+benchmarks/**
+logs/**
+resources/**
+!resources/datavzrd/**
+!resources/summary_plot.json
+results/**
+.snakemake/**

.test/config/config.yaml

@@ -0,0 +1,40 @@
+samples: config/samples.tsv
+units: config/units.tsv
+
+reference:
+  # NOTE: ANY CHANGE OF SPECIES, RELEASE OR BUILD IN THIS TESTING
+  #       CONFIG.YAML REQUIRES ADJUSTING THE FILENAME OF RESOURCE/*.FASTA
+  # Ensembl species name
+  species: homo_sapiens
+  # Genome build
+  build: GRCh38
+  # Ensembl release
+  release: 107
+  # for available downloads, please browse either of these views:
+  # * http://repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
+  # * http://repeatmasker.org/genomicDatasets/RMGenomicDatasetsAlt.html
+  repeat_masker_download_link: "http://www.repeatmasker.org/genomes/hg38/RepeatMasker-rm406-dfam2.0/hg38.fa.out.gz"
+
+
+cyrcular:
+  # minimum read depth (used during covered segment identification)
+  min_read_depth: 2
+  # minimum number of split reads (edges with less than this number will be removed from the graph)
+  min_split_reads: 5
+  # maximum number of plausible circular paths generated for each strongly connected component of the graph
+  max_paths_per_component: 15
+  # maximum deletion length which is encoded as an edge / a breakend event. Can be useful for unmapped regions in the reference.
+  max_deletion_length: 10000
+
+filter:
+  # varlociraptor fdr control
+  fdr-control:
+    threshold: 0.1
+    mode: local-smart
+    events:
+      circular:
+        varlociraptor:
+          - present
+  circles:
+    min-length: 100
+    max-length: 50_000_000

.test/config/samples.tsv

@@ -0,0 +1,2 @@
+group	sample_name	platform
+example	example	nanopore

.test/config/units.tsv

@@ -0,0 +1,2 @@
+sample_name	unit_name	fq1	fq2
+example	0	data/example_reads.fastq.gz	

resources/example_ref.fasta → .test/resources/homo_sapiens.GRCh38.107.fasta

@@ -1,4 +1,113 @@
->M
+>2
+AGGCTGTGACAGTCATCTGTCTGGACGCGCTGGGTGGATGCGGGGGGCTCCTGGGAACTG
+TGTTGGAGCCGAGCAAGCGCTAGCCAGGCGCAAGCGCGCACAGACTGTAGCCATCCGAGG
+ACACCCCCGCCCCCCCGGCCCACCCGGAGACACCCGCGCAGAATCGCCTCCGGATCCCCT
+GCAGTCGGCGGGAGGTAAGGAGCAGGGCTTGCAAACCGCCCGGCGCCCAGGGAAGCGACG
+AGCGCCGGGGCAAGGCAAGCCCTGGACGGGATTGCGACGTGCGCACCGGGCGCCCTAATA
+TGCCCGGGGGACTGTTTCTGCTTCCGAAACAAAACCATCTCTGGGTTTTCCCAGAAAAGC
+CAGTTCCAGCCCCGAAGGCATCCTGGCTAGAGGAGACCCGCCCTAATCCTTTTGCAGCCC
+TTACCGGGGGGAGTAATGGCTTCTGCGAAAAGAAATTCCCTCGGCTCTAGAAGATCTGTC
+TGTGTTTGAGCTGTCGGAGAGCCGGTGCGTCCCCACCCCAGGCTGGGGTTCTTCTCCAAA
+GGGTGCCCCTGGAGGAAGAAGAGGGGGGGATTAGGCAGGGCGAGGCCGCCGCGGTCGCAA
+TCTGGGTCACGGCTGCTCCAGCTTGGAGGAGAGGCGGCTCTCCCGGCGACCCTCCTCGCG
+CGGGCGCCCCTGCCATTCCCGGGAACAGGGGCTCAGCCTCTCCCTCCCTGGAAGAGGACG
+TTGTCGTGGGTTTGGAAGAGCAGGGGTGGGCTTAGAGAGCTTCCAATTAAGCTATTGGCA
+GGAGTATCCCTGCAGCGGGTGAATGCCGAGGGGCGTTTGCTCAAATTTGGGGAGGGGAAG
+GATTTGTGGATATGGGTGTCTGTTGTTGGTCTCTGTCTAGAGAAAGGCTTTTTTTTATTT
+GCAAAGTTTTCTAAATCCCCTGCTATCATTTGCACTCCTGAGGTTGCATTTTTACAAAGG
+GGGTAGAAGGTACTCCAAATACCATTCCCGGTAGCTGGGTCGGAGAGCCTGGGGCTTCCC
+CTGAGCAGCCGGCCCCACACCGCTGCGAGTGCGGTTGTCTGCGTGCTCGTGAGAGCTAGA
+ATTCTGCAGCCAGGAACAGCCCCCTCCCCCAGGCAGTGCCTTGTGTGAATGAAATGGCAG
+TTTCCAAAGTTGCGGAGCCTCGCCACCACCCCCTGCATCTGCATGCCCCCTCCCACCCCC
+TGTCGTAGACAGCTTGTACACAAAAGGAGGGCGGGAGGGAGGGAGCGAGAGGCACAACTT
+CCTCCACCTTCGGGAGCAGTGGGCAGAGTGGGGGGCTTGGAGGGAAGATTGGGGAACCTG
+GTTAGAGGGGGCGCCCATTGCCTATCCCCTCGGTCTGCCCCGTTTGCCCACCCTCTCCGG
+TGTGTCTGTCGGTTGCAGTGTTGGAGGTCGGCGCCGGCCCCCGCCTTCCGCGCCCCCCAC
+GGGAAGGAAGCACCCCCGGTATTAAAACGAACGGGGCGGAAAGAAGCCCTCAGTCGCCGG
+CCGGGAGGCGAGCCGATGCCGAGCTGCTCCACGTCCACCATGCCGGGCATGATCTGCAAG
+AACCCAGACCTCGAGTTTGACTCGCTACAGCCCTGCTTCTACCCGGACGAAGATGACTTC
+TACTTCGGCGGCCCCGACTCGACCCCCCCGGGGGAGGACATCTGGAAGAAGTTTGAGCTG
+CTGCCCACGCCCCCGCTGTCGCCCAGCCGTGGCTTCGCGGAGCACAGCTCCGAGCCCCCG
+AGCTGGGTCACGGAGATGCTGCTTGAGAACGAGCTGTGGGGCAGCCCGGCCGAGGAGGAC
+GCGTTCGGCCTGGGGGGACTGGGTGGCCTCACCCCCAACCCGGTCATCCTCCAGGACTGC
+ATGTGGAGCGGCTTCTCCGCCCGCGAGAAGCTGGAGCGCGCCGTGAGCGAGAAGCTGCAG
+CACGGCCGCGGGCCGCCAACCGCCGGTTCCACCGCCCAGTCCCCGGGAGCCGGCGCCGCC
+AGCCCTGCGGGTCGCGGGCACGGCGGGGCTGCGGGAGCCGGCCGCGCCGGGGCCGCCCTG
+CCCGCCGAGCTCGCCCACCCGGCCGCCGAGTGCGTGGATCCCGCCGTGGTCTTCCCCTTT
+CCCGTGAACAAGCGCGAGCCAGCGCCCGTGCCCGCAGCCCCGGCCAGTGCCCCGGCGGCG
+GGCCCTGCGGTCGCCTCGGGGGCGGGTATTGCCGCCCCAGCCGGGGCCCCGGGGGTCGCC
+CCTCCGCGCCCAGGCGGCCGCCAGACCAGCGGCGGCGACCACAAGGCCCTCAGTACCTCC
+GGAGAGGACACCCTGAGCGATTCAGGTAAAGACCGAACTCGGGTCCGGCTGCCTCCCTGG
+GGCACTGGACCCCGGGTCGCGTCCCCTTTGTTAGTGCTCGTATGTCTTGGCCTGGGGAGC
+ATTTTGGAGGCAGTGCTAGGGGCAGAGAGGTCCTGTTTCCCCCAAGTCTCTCCTCGGGGT
+AAAGAGAAGGGGCTGAGAGAATGCCGTTGCAAAAGGGGTGCTCTCCAATTCTCGCCTTCA
+CTAAAGTTCCTTCCACCCTCTCCTGGGGAGCCCTCCTCTAGGCCATCACGGGCCCTCACC
+CGGTCCCCCACCTCTCTTTTGCAGCGCAGTCTGAGGAATAAAATTGGAGAAAGTTGGTGG
+CTAAACCGGGTGGGGGTTTAGGGGGTTGCTGGGTGCACTGCCTGGACAGAAACCTGTTAG
+CGCAGGGGTGAAAGGGACTCTCTGGCCCAGGTCAGGGGAGGGAAAGACATCCCGAGAAGA
+TTCAAGGGCTGTGCAAAGCCCTGTTTAAGGCGCAGGAACTTATAGGAGGGTTGCACAGAT
+GGCTAGAGCCGATTTTCTATTCTTTTTCTTTTTCTTTTTTTTTTTTTTTCAAATGTCGGT
+ACCTTTCCCTTCCCCCATCCTCGGTGGGTGGTGGGCTATTTGCTCCTGGTGCGTGGCCAG
+CAGGCGGCGATATGCGAGGCCAGCAGGCGGGCCCGGGATCTGAAAGGCTGGGGGTGGTGG
+GGGCACCCTCCCTCCCTCCATTCAGCAGCTGGCTGCAAGTGCAACAGCAGTTGTGTACAT
+TCTCAGGGGGCCTCCTCTTTCCAGTGTGCAGTGGAAACTGGCTGTAGTTTTGTCTTCCAG
+CCTGAATTCCAGGCCTAATTTGAGATGTGAGTTGTATCTGTAACCCAGTGCCCTTGAAGG
+TGAGGGCAGGCACTCAGCAGCCTCTCCAGGAAGGCTCACATCCTGGGAGGACTCACTGAT
+TAGTTCTATTGTGTTCATTTGTCTGTGTCTTAAGCTGAAGGGAAGAGTTAAAACCAAGCC
+TTTCCCTGGGGGTCTGGATGAACAGAACTCAACCCAAAGAGTGGCATTGCCTTGTCCTTG
+GAGCAGGGAGCTGGGACCCCCCTTGGACTTTGAAAACCAGTGTTTTCAGAATGCAGGTGG
+ATAACAAGCCTAAATTTACTTCTGGGCTGAGGAGAGATCTTTGAGGCTCCTGGAAGGAAA
+CTTGGTGATAAGCCTCCAGTTTGAAACGGCTCTGTCCCTTTAATGTCTGTGCCTTGACAG
+CTTTTGGTGAGGAAGCACTTCCTTCCAACAGCTGTCTTCTTGGCAGAAAACCAAAACATT
+GGCTTAAAGGGACCCACAGACTGGAACAGCCTCACATTTCGGCTTTAGAACAAATCCCAC
+AATTGTTCAGCTTTCCGGTCCCCTTCAGATCAAGCAGAAGATATGTTTTGATTTTCATGC
+TTGTATTTTAAACAATAATTTTCTACCCCAGCGTGGTAGTCAATGAGGAGAGAGGGGAAG
+AATGCGCACATGATGCTACACGTTTCTGTTGTTGCTGTTATTATTGGTGGCTTTGAGGAG
+AGCTGCTCCCATTTGGGGGTTTATACCAACTGTGGATTATGGCTTTGTCATTAAGATTTG
+ATCTTTGTTAAATGAAAAACTGTTTATTGTATAAAACTCAGGTTTGTGGACGAAAAGTTG
+TTTTTTTTCTTCAGTTAATTAAATTGTTCCTCAAGTTTGTTTAAGGACTTAAAATCAAAC
+ACAACCATGTGTAAACTGCTAAATGAGGCTCCTAAAATGAGAGGCCTCAACTCTTTAAGT
+GTGGAGCTAGAAATGTAAATAAGTCCACAGGGCAGACTGGTGATTATGATAAAAGCTACC
+ATTTACTGAGCATCTGTCTACTAGGCTCAGCTCTATGCTAAGTCTACATGTTATCTGTCA
+AAGTGGTATCATCCCCATTTAATAGCTGAGGAAACAGAGGCTTAGAAAGGCTGGGTAACT
+TGACCAGGGTCATGCAACTAGTCTGCGGTGGAGCCAGGATTCTGTCTGACCCTAAAGGCC
+AAGTTCTTTATATTTATTTCTACCACCTGCTAAAGTCTTGAATGGAGGCTGAAAGCACAG
+TTGGGGTATGGGGAAGAAAAATATATATACATACATATATGTATATGTATGTATGTATGT
+ATGGGGGGTTGTTTTGTTTTTGTTTTTGATAAGGAGTTTTGCTCTTGTTGCCCAGGCTGG
+AGTGCAGTGGTATGATCTGGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGTCATTCTC
+CTGCCTCAGCCTCCCGAGTAGCTGGGATTACCGGAGCATGCCACCACACCCAGCAAAGTT
+TTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTGGCCAGGCTGATCTTGAACTCCTCA
+TCTCAGGTGATCTGCCCGCCTCCGCTTCCCAAAGTGCTGGGATTACAGGTGTGAGTCACC
+GCGTCCGGCCTACAGATATATTTAATTTAAAGAGATCTAAAACAAATACAAAACTGTCCA
+CATCTATGTTGATGGACCCATAAAAATAGCAGTCTGCCAGGGTCTGCCGGAAGAGACAGA
+TAAGCATACATATTAACATGGATATATATGTGAATTTCATTCAAATGGTTCTCACATGAG
+AGTAACTAGCATCTTTCTCTCAGATGATGAAGATGATGAAGAGGAAGATGAAGAGGAAGA
+AATCGACGTGGTCACTGTGGAGAAGCGGCGTTCCTCCTCCAACACCAAGGCTGTCACCAC
+ATTCACCATCACTGTGCGTCCCAAGAACGCAGCCCTGGGTCCCGGGAGGGCTCAGTCCAG
+CGAGCTGATCCTCAAACGATGCCTTCCCATCCACCAGCAGCACAACTATGCCGCCCCCTC
+TCCCTACGTGGAGAGTGAGGATGCACCCCCACAGAAGAAGATAAAGAGCGAGGCGTCCCC
+ACGTCCGCTCAAGAGTGTCATCCCCCCAAAGGCTAAGAGCTTGAGCCCCCGAAACTCTGA
+CTCGGAGGACAGTGAGCGTCGCAGAAACCACAACATCCTGGAGCGCCAGCGCCGCAACGA
+CCTTCGGTCCAGCTTTCTCACGCTCAGGGACCACGTGCCGGAGTTGGTAAAGAATGAGAA
+GGCCGCCAAGGTGGTCATTTTGAAAAAGGCCACTGAGTATGTCCACTCCCTCCAGGCCGA
+GGAGCACCAGCTTTTGCTGGAAAAGGAAAAATTGCAGGCAAGACAGCAGCAGTTGCTAAA
+GAAAATTGAACACGCTCGGACTTGCTAGACGCTTCTCAAAACTGGACAGTCACTGCCACT
+TTGCACATTTTGATTTTTTTTTTAAACAAACATTGTGTTGACATTAAGAATGTTGGTTTA
+CTTTCAAATCGGTCCCCTGTCGAGTTCGGCTCTGGGTGGGCAGTAGGACCACCAGTGTGG
+GGTTCTGCTGGGACCTTGGAGAGCCTGCATCCCAGGATGCTGGGTGGCCCTGCAGCCTCC
+TCCACCTCACCTCCATGACAGCGCTAAACGTTGGTGACGGTTGGGAGCCTCTGGGGCTGT
+TGAAGTCACCTTGTGTGTTCCAAGTTTCCAAACAACAGAAAGTCATTCCTTCTTTTTAAA
+ATGGTGCTTAAGTTCCAGCAGATGCCACATAAGGGGTTTGCCATTTGATACCCCTGGGGA
+ACATTTCTGTAAATACCATTGACACATCCGCCTTTTGTATACATCCTGGGTAATGAGAGG
+TGGCTTTTGCGGCCAGTATTAGACTGGAAGTTCATACCTAAGTACTGTAATAATACCTCA
+ATGTTTGAGGAGCATGTTTTGTATACAAATATATTGTTAATCTCTGTTATGTACTGTACT
+AATTCTTACACTGCCTGTATACTTTAGTATGACGCTGATACATAACTAAATTTGATACTT
+ATATTTTCGTATGAAAATGAGTTGTGAAAGTTTTGAGTAGATATTACTTTATCACTTTTT
+GAACTAAGAAACTTTTGTAAAGAAATTTACTATATATATATGCCTTTTTCCTAGCCTGTT
+TCTTCCTGTTAATGTATTTGTTCATGTTTGGTGCATAGAACTGGGTAAATGCAAAGTTCT
+GTGTTTAATTTCTTCAAAATGTATATATTTAGTGCTGCATCTTATAGCACTTTGAAATAC
+CTCATGTTTATGAAAATAAATAGCTTAAAATTAAATGA
+>MT
 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT
 CGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC
 GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT

.test/resources/scenarios/illumina_circle_scenario.yaml

@@ -0,0 +1 @@
+../../../resources/scenarios/illumina_circle_scenario.yaml

.test/resources/scenarios/nanopore_circle_scenario.yaml

@@ -0,0 +1 @@
+../../../resources/scenarios/nanopore_circle_scenario.yaml

.test/resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml

@@ -0,0 +1 @@
+../../../resources/scenarios/nanopore_illumina_joint_circle_scenario.yaml

CITATION.cff

@@ -0,0 +1,45 @@
+cff-version: 1.2.0
+message: "If you use this workflow, please cite the article from preferred-citation and the workflow itself."
+authors:
+- family-names: "Hartmann"
+  given-names: "Till"
+  orcid: "https://orcid.org/0000-0002-6993-347X"
+- family-names: "Lähnemann"
+  given-names: "David"
+  orcid: "https://orcid.org/0000-0002-9138-4112"
+title: "snakemake-workflows/cyrcular-calling"
+version: 1.2.0
+doi: Zenodo DOI TBD
+date-released: 2023-04-06
+url: "https://github.com/snakemake-workflows/cyrcular-calling"
+preferred-citation:
+  type: article
+  authors:
+  - family-names: "Tüns"
+    given-names: "Alicia Isabell"
+    orcid: "https://orcid.org/0000-0003-0025-1304"
+  - family-names: "Hartmann"
+    given-names: "Till"
+    orcid: "https://orcid.org/0000-0002-6993-347X"
+  - family-names: "Magin"
+    given-names: "Simon"
+  - family-names: "Chamorro González"
+    given-names: "Rocío"
+    orcid: "https://orcid.org/0000-0002-5653-7259"
+  - family-names: "Henssen"
+    given-names: "Anton George"
+    orcid: "https://orcid.org/0000-0003-1534-778X"
+  - family-names: "Rahmann"
+    given-names: "Sven"
+    orcid: "https://orcid.org/0000-0002-8536-6065"
+  - family-names: "Schramm"
+    given-names: "Alexander"
+    orcid: "https://orcid.org/0000-0001-7670-7529"
+  - family-names: "Köster"
+    given-names: "Johannes"
+    orcid: "https://orcid.org/0000-0001-9818-9320"
+  doi: "10.3389/fgene.2022.867018"
+  journal: "Frontiers in Genetics"
+  month: 05
+  year: 2022
+  title: "Detection and Validation of Circular DNA Fragments Using Nanopore Sequencing"

README.md

@@ -1,7 +1,8 @@
 # Snakemake workflow: cyrcular-calling
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥6.15.0-brightgreen.svg)](https://snakemake.github.io)
-
+[![Tests](https://github.com/snakemake-workflows/cyrcular-calling/actions/workflows/main.yaml/badge.svg)](https://github.com/snakemake-workflows/cyrcular-calling/actions/workflows/main.yaml)
+[![Conventional Commits](https://img.shields.io/badge/Conventional%20Commits-1.0.0-%23FE5196?logo=conventionalcommits&logoColor=white)](https://conventionalcommits.org)
 
 A Snakemake workflow for ecDNA detection in nanopore sequencing reads derived from DNA samples enriched for circular DNA.
 

config/config.yaml

@@ -1,23 +1,20 @@
-calling:
-  samples: config/samples.tsv
-  units: config/units.tsv
+samples: config/samples.tsv
+units: config/units.tsv
 
-  reference:
-    # if `path` is not set, name should just be "genome" atm.
-    name: "example_ref"
-    # Custom path overrides everything below that, if file exists
-    # (in that case, path must match "resources/" + name + ".fasta")
-    path: "resources/example_ref.fasta"
-    # The first n entries of the FASTA will be considered.
-    n_chromosomes: 25
-    # Ensembl species name
-    species: homo_sapiens
-    # Ensembl release
-    release: 100
-    # Genome build
-    build: GRCh38
+reference:
+  # Ensembl species name
+  species: homo_sapiens
+  # Genome build
+  build: GRCh38
+  # Ensembl release
+  release: 107
+  # for available downloads, please browse either of these views:
+  # * http://repeatmasker.org/genomicDatasets/RMGenomicDatasets.html
+  # * http://repeatmasker.org/genomicDatasets/RMGenomicDatasetsAlt.html
+  repeat_masker_download_link: "http://www.repeatmasker.org/genomes/hg38/RepeatMasker-rm406-dfam2.0/hg38.fa.out.gz"
 
 
+cyrcular:
   # minimum read depth (used during covered segment identification)
   min_read_depth: 2
   # minimum number of split reads (edges with less than this number will be removed from the graph)
@@ -27,12 +24,15 @@ calling:
   # maximum deletion length which is encoded as an edge / a breakend event. Can be useful for unmapped regions in the reference.
   max_deletion_length: 10000
 
-  filter:
-    # varlociraptor fdr control
-    fdr-control:
-      threshold: 0.1
-      local: true
-      events:
-        circular:
-          varlociraptor:
-            - present
+filter:
+  # varlociraptor fdr control
+  fdr-control:
+    threshold: 0.1
+    mode: local-smart
+    events:
+      circular:
+        varlociraptor:
+          - present
+  circles:
+    min-length: 100
+    max-length: 50_000_000