Update GFA reader to support GFA v1.2 paths #117

Workflow file for this run

.github/workflows/single_cell.yml at 511bb15

	name: SPAdes single-cell datasets tests

	on:
	workflow_dispatch:
	pull_request:
	paths-ignore:
	- 'docs/**'
	- 'mkdocs.yml'
	push:
	tags:
	- '*'
	schedule:
	- cron: '0 12 * * 2,6'

	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

	sc-ecoli-deeptrench:
	name: 'Single-cell E.coli deeptrench'
	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/SC_E.coli_deeptrench.info

	sc-ecoli-jgi-lane7:
	name: 'Single-cell E.coli JGI lane 7'
	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/SC_E.coli_JGI_lane7.info

	sc-ecoli-jgi-lane7-2libs:
	name: 'Single-cell E.coli JGI lane 7 2 libraries'
	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/SC_E.coli_JGI_lane7_2lib.info

	sc-ctg-ecoli-ucsd-lane1:
	name: 'Single-cell+contigs E.coli UCSD lane 1'
	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/SC_CGT_E.coli_UCSD_lane1.info

	sc-pheparinus-jgi-lane7:
	name: 'Single-cell P.heparinus JGI lane 7'
	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/SC_P.heparinus_JGI_lane7.info

	sc-mruber-jgi-lane9:
	name: 'Single-cell M.ruber JGI lane 9'
	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/SC_M.ruber_JGI_lane9.info

	sc-pmarinus:
	name: 'Single-cell P.marinus'
	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/SC_P.marinus.info

	sc-pb-tm6:
	name: 'Single-cell+PacBio TM6'
	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/SC_PB_Tm6.info

	sc-se-pmarinus:
	name: 'Single-cell single-end P.marinus'
	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/SC_SE_P.marinus.info

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Update GFA reader to support GFA v1.2 paths #117

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Update GFA reader to support GFA v1.2 paths #117

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Workflow file for this run