Update GFA reader to support GFA v1.2 paths #115

Workflow file for this run

.github/workflows/mate_pairs.yml at 21595d4

	name: SPAdes mate-pairs tests

	on:
	workflow_dispatch:
	pull_request:
	paths-ignore:
	- 'docs/**'
	- 'mkdocs.yml'
	push:
	tags:
	- '*'
	schedule:
	- cron: '0 14 * * 3,6'

	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/[email protected]
	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

	iso-ecoli-is220:
	name: 'Isolated 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/ISO_E.coli_is220.info

	iso-lgasseri:
	name: 'Isolated L.gasseri'
	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/ISO_L.gasseri.info

	mp-amirum:
	name: '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/MP_A.mirum.info

	mp-lgasseri:
	name: 'Mate-pairs L.gasseri'
	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/MP_L.gasseri.info

	nx-kpneumoniae:
	name: 'Nextera mate-pairs 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/NX_K.pneumoniae.info

	nx-rsphaeroides:
	name: 'Nextera mate-pairs R.sphaeroides'
	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/NX_R.sphaeroides.info

	mp-ssmaragdinae:
	name: 'Mate-pairs 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/MP_S.smaragdinae_quake.info

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Update GFA reader to support GFA v1.2 paths #115

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Update GFA reader to support GFA v1.2 paths #115

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Workflow file for this run