add adapter specification #471

Workflow file for this run

	name: Test Harpy Modules

	on:
	push:
	branches:
	- 'main'
	pull_request:
	branches:
	- main

	# Cancel in progress workflows on pull_requests.
	# https://docs.github.com/en/actions/using-jobs/using-concurrency#example-using-a-fallback-value
	concurrency:
	group: ${{ github.workflow }}-${{ github.head_ref \|\| github.run_id }}
	cancel-in-progress: true

	env:
	CACHE_NUMBER: 0 # increase to reset cache manually

	jobs:
	changes:
	name: Detect File Changes
	runs-on: ubuntu-latest
	# Required permissions
	permissions:
	pull-requests: read
	# Set job outputs to values from filter step
	outputs:
	preflight: ${{ steps.filter.outputs.preflight }}
	deconvolve: ${{ steps.filter.outputs.deconvolve }}
	demux: ${{ steps.filter.outputs.demux }}
	qc: ${{ steps.filter.outputs.qc }}
	bwa: ${{ steps.filter.outputs.bwa }}
	ema: ${{ steps.filter.outputs.ema }}
	strobealign: ${{ steps.filter.outputs.strobealign }}
	mpileup: ${{ steps.filter.outputs.mpileup }}
	freebayes: ${{ steps.filter.outputs.freebayes }}
	leviathan: ${{ steps.filter.outputs.leviathan }}
	naibr: ${{ steps.filter.outputs.naibr }}
	impute: ${{ steps.filter.outputs.impute }}
	phase: ${{ steps.filter.outputs.phase }}
	simvars: ${{ steps.filter.outputs.simvars }}
	simreads: ${{ steps.filter.outputs.simreads }}
	assembly: ${{ steps.filter.outputs.assembly }}
	other: ${{ steps.filter.outputs.other }}
	container: ${{ steps.filter.outputs.container }}
	modules: ${{ steps.filter.outputs.modules }}
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	- name: Check Which Files Have Changes
	uses: dorny/paths-filter@v3
	id: filter
	with:
	base: 'main'
	filters: .github/filters.yml

	pkgbuild:
	needs: changes
	name: Build/Cache Container
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	run: rm -rf /opt/hostedtoolcache
	- name: Rebuild Dockerfile
	id: rebuild
	if: ${{ needs.changes.outputs.container == 'true' }}
	shell: micromamba-shell {0}
	run: harpy containerize
	- name: Set up Docker Buildx
	id: buildx
	if: ${{ steps.rebuild.outcome == 'success' }}
	uses: docker/setup-buildx-action@v3
	- name: Login to Docker Hub
	id: dockerhub
	if: ${{ steps.buildx.outcome == 'success' }}
	uses: docker/login-action@v3
	with:
	username: ${{ secrets.DOCKERHUB_USERNAME }}
	password: ${{ secrets.DOCKERHUB_TOKEN }}
	- name: Build and Push to Dockerhub
	if: ${{ steps.dockerhub.outcome == 'success' }}
	uses: docker/build-push-action@v5
	with:
	context: .
	push: true
	tags: pdimens/harpy:latest
	- name: Pull Image Locally
	id: singularity
	shell: micromamba-shell {0}
	if: ${{ needs.changes.outputs.modules == 'true' }}
	run: harpy qc --skip-reports --quiet test/fastq/sample1.*.fq.gz
	- name: Create Singularity Artifact
	if: ${{ steps.singularity.outcome == 'success' }}
	uses: actions/upload-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity/*.simg
	retention-days: 1

	dmux_gen1:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.demux == 'true' && needs.pkgbuild.result == 'success' }}
	name: demux gen1
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: harpy demultiplex
	shell: micromamba-shell {0}
	run: harpy demultiplex gen1 --quiet --schema test/demux/samples.schema test/demux/Undetermined_S0_L004_R* test/demux/Undetermined_S0_L004_I*

	preflight:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.preflight == 'true' && needs.pkgbuild.result == 'success' }}
	name: preflight
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: test preflight fastq
	shell: micromamba-shell {0}
	run: harpy preflight fastq test/fastq
	- name: test preflight bam
	if: always()
	shell: micromamba-shell {0}
	run: harpy preflight bam --quiet test/bam

	qc:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.qc == 'true' && needs.pkgbuild.result == 'success' }}
	name: qc
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: harpy qc
	shell: micromamba-shell {0}
	run: harpy qc -x "--low_complexity_filter" --quiet test/fastq
	- name: harpy qc all options
	shell: micromamba-shell {0}
	run: harpy qc -a auto -d -c 21,40,3,0 --quiet test/fastq
	deconvolve:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.deconvolve == 'true' && needs.pkgbuild.result == 'success' }}
	name: deconvolve
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: harpy deconvolve
	shell: micromamba-shell {0}
	run: harpy deconvolve --quiet test/fastq
	bwa:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.bwa == 'true' && needs.pkgbuild.result == 'success' }}
	name: align BWA
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: test bwa
	shell: micromamba-shell {0}
	run: harpy align bwa --quiet -g test/genome/genome.fasta.gz -x "-A 2" test/fastq

	ema:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.ema == 'true' && needs.pkgbuild.result == 'success' }}
	name: align EMA
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: test ema
	shell: micromamba-shell {0}
	run: harpy align ema --quiet --ema-bins 150 -g test/genome/genome.fasta.gz test/fastq

	strobe:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.strobealign == 'true' && needs.pkgbuild.result == 'success' }}
	name: align strobe
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: test strobealign
	shell: micromamba-shell {0}
	run: harpy align strobe --quiet -l 125 -g test/genome/genome.fasta.gz test/fastq

	mpileup:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.mpileup == 'true' && needs.pkgbuild.result == 'success' }}
	name: mpileup
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: snp mpileup
	shell: micromamba-shell {0}
	run: harpy snp mpileup --quiet -r test/positions.bed -g test/genome/genome.fasta.gz -x "--ignore-RG" test/bam
	- name: snp mpileup-pop
	shell: micromamba-shell {0}
	run: harpy snp mpileup --quiet -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups test/bam

	freebayes:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.freebayes == 'true' && needs.pkgbuild.result == 'success' }}
	name: freebayes
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: snp freebayes
	shell: micromamba-shell {0}
	run: harpy snp freebayes --quiet -r test/positions.bed -g test/genome/genome.fasta.gz -x "-g 200" test/bam
	- name: snp freebayes-pop
	shell: micromamba-shell {0}
	run: harpy snp freebayes --quiet -r test/positions.bed -o SNP/poptest -g test/genome/genome.fasta.gz -p test/samples.groups test/bam

	impute:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.impute == 'true' && needs.pkgbuild.result == 'success' }}
	name: impute
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: impute
	shell: micromamba-shell {0}
	run: harpy impute --quiet --vcf test/vcf/test.bcf -p test/stitch.params test/bam
	- name: impute from vcf
	shell: micromamba-shell {0}
	if: always()
	run: harpy impute --quiet --vcf-samples -o vcfImpute --vcf test/vcf/test.bcf -p test/stitch.params test/bam

	phase:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.phase == 'true' && needs.pkgbuild.result == 'success' }}
	name: phase
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: phase
	shell: micromamba-shell {0}
	run: harpy phase --quiet --vcf test/vcf/test.bcf -x "--max_iter 10001" test/bam
	- name: phase with indels
	shell: micromamba-shell {0}
	if: always()
	run: harpy phase --quiet --vcf test/vcf/test.bcf -o phaseindel -g test/genome/genome.fasta.gz test/bam
	- name: phase from vcf
	shell: micromamba-shell {0}
	if: always()
	run: \|
	cp test/bam/sample1.bam test/bam/pineapple.bam && rename_bam.py -d pineapple1 test/bam/pineapple.bam
	harpy phase --quiet --vcf-samples -o phasevcf --vcf test/vcf/test.bcf test/bam

	leviathan:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.leviathan == 'true' && needs.pkgbuild.result == 'success' }}
	name: sv leviathan
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: leviathan
	shell: micromamba-shell {0}
	run: harpy sv leviathan --quiet -s 100 -b 1 -g test/genome/genome.fasta.gz -x "-M 2002" test/bam
	continue-on-error: true
	- name: leviathan-pop
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv leviathan --quiet -s 100 -b 1 -g test/genome/genome.fasta.gz -o SV/leviathanpop -p test/samples.groups test/bam

	naibr:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.naibr == 'true' && needs.pkgbuild.result == 'success' }}
	name: sv naibr
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: naibr
	shell: micromamba-shell {0}
	run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/naibr -x "-min_sv 5000" test/bam_phased && rm -r Genome
	- name: naibr pop
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/pop -p test/samples.groups test/bam_phased && rm -r Genome
	- name: naibr with phasing
	if: always()
	shell: micromamba-shell {0}
	run: \|
	harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/phase -v test/vcf/test.phased.bcf test/bam && rm -r Genome
	- name: naibr pop with phasing
	if: always()
	shell: micromamba-shell {0}
	run: harpy sv naibr --quiet -g test/genome/genome.fasta.gz -o SV/phasepop -v test/vcf/test.phased.bcf -p test/samples.groups test/bam && rm -r Genome


	simulate_variants:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.simvars == 'true' && needs.pkgbuild.result == 'success' }}
	name: simulate variants
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: simulate random snps/indels
	shell: micromamba-shell {0}
	run: \|
	harpy simulate snpindel --quiet --snp-count 10 --indel-count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate snpindel --quiet --prefix Simulate/snpvcf --snp-vcf Simulate/snpindel/haplotype_1/sim.hap1.snp.vcf --indel-vcf Simulate/snpindel/haplotype_1/sim.hap1.indel.vcf test/genome/genome.fasta.gz
	- name: simulate inversions
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate inversion --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate inversion --quiet --prefix Simulate/invvcf --vcf Simulate/inversion/haplotype_1/sim.hap1.inversion.vcf test/genome/genome.fasta.gz
	- name: simulate cnv
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate cnv --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate cnv --quiet --prefix Simulate/cnvvcf --vcf Simulate/cnv/haplotype_1/sim.hap1.cnv.vcf test/genome/genome.fasta.gz
	- name: simulate translocations
	shell: micromamba-shell {0}
	if: always()
	run: \|
	harpy simulate translocation --quiet --count 10 -z 0.5 test/genome/genome.fasta.gz
	harpy simulate translocation --quiet --prefix Simulate/transvcf --vcf Simulate/translocation/haplotype_1/sim.hap1.translocation.vcf test/genome/genome.fasta.gz

	simulate_linkedreads:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.simreads == 'true' && needs.pkgbuild.result == 'success' }}
	name: simulate linkedreads
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: simulate linked reads
	shell: micromamba-shell {0}
	run: \|
	haplotag_barcodes.py -n 14000000 > test/haplotag.bc
	harpy simulate linkedreads --quiet -t 4 -n 2 -b test/haplotag.bc -l 100 -p 50 test/genome/genome.fasta.gz test/genome/genome2.fasta.gz

	assembly:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.assembly == 'true' && needs.pkgbuild.result == 'success' }}
	name: metassembly
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: Download Singularity Artifact
	uses: actions/download-artifact@v4
	with:
	name: deps-image
	path: .snakemake/singularity
	- name: test assembly
	shell: micromamba-shell {0}
	run: harpy assembly --quiet -r 4000 test/fastq/sample1.*
	- name: test metassembly
	shell: micromamba-shell {0}
	run: harpy metassembly --quiet -r 4000 test/fastq/sample1.*
	- name: test metassembly without barcodes
	shell: micromamba-shell {0}
	run: harpy metassembly --ignore-bx --quiet -r 4000 test/fastq/sample1.*

	extras:
	needs: [changes, pkgbuild]
	if: ${{ needs.changes.outputs.other == 'true' && needs.pkgbuild.result == 'success' }}
	name: harpy extras
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: Setup Mamba
	uses: mamba-org/setup-micromamba@v1
	env:
	ACTIONS_STEP_DEBUG: true
	with:
	init-shell: bash
	generate-run-shell: true
	environment-file: resources/harpy.yaml
	cache-environment: true
	post-cleanup: 'all'
	log-level: error
	- name: Install Harpy
	shell: micromamba-shell {0}
	run: \|
	python3 -m pip install --upgrade build && python3 -m build
	pip install dist/*.whl
	resources/buildforCI.sh
	- name: Clear Space
	uses: jlumbroso/free-disk-space@main
	- name: harpy imputeparams
	shell: micromamba-shell {0}
	run: harpy imputeparams -o params.file
	- name: harpy popgroup
	shell: micromamba-shell {0}
	run: harpy popgroup test/fastq
	- name: harpy downsample bam
	shell: micromamba-shell {0}
	run: harpy downsample -d 1 --random-seed 699 --quiet test/bam/sample1.bam
	- name: harpy downsample fastq
	shell: micromamba-shell {0}
	run: harpy downsample -d 1 --quiet test/fastq/sample1.*gz
	- name: harpy hpc
	shell: micromamba-shell {0}
	run: \|
	harpy hpc slurm
	harpy hpc googlebatch
	harpy hpc lsf
	harpy hpc htcondor

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