Write GFA header #43

Workflow file for this run

.github/workflows/long_reads.yml at b5b8852

	name: SPAdes long-read tests

	on:
	workflow_dispatch:
	pull_request:
	paths-ignore:
	- 'docs/**'
	push:
	tags:
	- '*'
	schedule:
	- cron: '0 23 * * 1,4'


	env:
	BUILD_TYPE: Release
	BUILD_DIR: ${{github.workspace}}/build
	INSTALL_DIR: ${{github.workspace}}/spades
	SRC_DIR: ${{github.workspace}}/src
	PKG: SPAdes-*-Linux

	jobs:
	build:
	runs-on: self-hosted
	name: '🚧 Build SPAdes'

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1

	- name: '⚙️ Install ccache'
	uses: hendrikmuhs/ccache-action@v1.2
	with:
	variant: sccache
	key: sccache-${{env.BUILD_TYPE}}

	- name: '⚙️ Configure CMake'
	run: >
	cmake
	-B ${{env.BUILD_DIR}}
	-S ${{env.SRC_DIR}}
	-DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
	-DCMAKE_INSTALL_PREFIX=${{env.INSTALL_DIR}}

	- name: '🚧 Build'
	run: >
	cmake
	--build ${{env.BUILD_DIR}}
	-j16
	-t package

	- name: '📦 Package'
	uses: actions/upload-artifact@v4
	with:
	name: build-artifacts
	path: \|
	${{env.BUILD_DIR}}/${{env.PKG}}.tar.gz

	ctg-ecoli-is220:
	name: 'Untrusted contigs E.coli is220'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/CTG_E.coli_is220.info

	ctg-geophsycobacter:
	name: 'Untrustred contigs Geophsycobacter'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/CTG_Geophsycobacter.info

	pb-amirum:
	name: 'PacBio A.mirum'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_A.mirum.info

	pb-mruber:
	name: 'PacBio M.ruber'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_M.ruber.info

	pb-mp-amirum:
	name: 'PacBio+Mate-pairs A.mirum'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_MP_A.mirum.info

	pb-mp-mruber:
	name: 'PacBio+Mate-pairs M.ruber'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_MP_M.ruber.info

	pb-ecoli:
	name: 'PacBio P4 E.coli is200'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_P4_E.coli_is220.info

	pb-pheparinus:
	name: 'PacBio P.heparinus'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/PB_P.heparinus.info

	tctg-kpneumoniae:
	name: 'Trusted contigs K.pneumoniae'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/TCTG_K.pneumoniae.info

	tctg-pstipitis:
	name: 'Trusted contigs P.stipitis'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/TCTG_P.stipitis.info

	tctg-ssmaragdinae:
	name: 'Trusted contigs S.smaragdinae quaked'
	runs-on: self-hosted
	needs: build

	steps:
	- name: '🧹 Cleanup'
	run: >
	set -e &&
	shopt -s dotglob &&
	rm -rf *

	- name: '🧰 Checkout'
	uses: actions/checkout@v4
	with:
	fetch-depth: 1
	- name: '📦 Download package'
	uses: actions/download-artifact@v4
	with:
	name: build-artifacts
	path: ${{env.INSTALL_DIR}}
	- name: '📦 Unpack package'
	working-directory: ${{env.INSTALL_DIR}}
	run: >
	tar -zxf ${{env.PKG}}.tar.gz
	- name: 'Assembly'
	run: >
	${{env.SRC_DIR}}/test/teamcity/github_runner.py
	--spades_path ${{env.INSTALL_DIR}}/${{env.PKG}}/bin
	--no_contig_archive
	/data/spades_tests/TCTG_S.smaragdinae_quake.info

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Write GFA header #43

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