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DSL2: Add mapAD

DSL2: Add mapAD #2802

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/eager') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
PARAMS:
- "-profile test,docker --preprocessing_tool fastp --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/fastp/adapters.fasta'"
- "-profile test,docker --preprocessing_tool adapterremoval --preprocessing_adapterlist 'https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/adapterremoval/adapterremoval_adapterlist.txt' --sequencing_qc_tool falco --run_genotyping --genotyping_tool 'freebayes' --genotyping_source 'raw'"
- "-profile test,docker --mapping_tool bwamem --run_mapdamage_rescaling --run_pmd_filtering --run_trim_bam --run_genotyping --genotyping_tool 'ug' --genotyping_source 'trimmed'"
- "-profile test,docker --mapping_tool bowtie2 --damagecalculation_tool mapdamage --damagecalculation_mapdamage_downsample 100 --run_genotyping --genotyping_tool 'hc' --genotyping_source 'raw'"
- "-profile test,docker --mapping_tool mapad"
- "-profile test,docker --mapping_tool circularmapper --skip_preprocessing --convert_inputbam --fasta_circular_target 'NC_007596.2' --fasta_circularmapper_elongationfactor 500"
- "-profile test_humanbam,docker --run_mtnucratio --run_contamination_estimation_angsd --snpcapture_bed 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/reference/Human/1240K.pos.list_hs37d5.0based.bed.gz' --run_genotyping --genotyping_tool 'pileupcaller' --genotyping_source 'raw'"
- "-profile test_humanbam,docker --run_sexdeterrmine --run_genotyping --genotyping_tool 'angsd' --genotyping_source 'raw'"
- "-profile test_multiref,docker" ## TODO add damage manipulation here instead once it goes multiref
steps:
- name: Check out pipeline code
uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
- name: Install Nextflow
uses: nf-core/setup-nextflow@v2
with:
version: "${{ matrix.NXF_VER }}"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
- name: Run pipeline with test data
# TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} --outdir ./results ${{ matrix.PARAMS }}