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Merge branch 'master' into public #4

Merge branch 'master' into public

Merge branch 'master' into public #4

Workflow file for this run

name: GitHub Actions CI
on:
push:
branches: [ master ]
paths-ignore:
- '**.md'
workflow_dispatch:
jobs:
linux-remote:
name: Linux test (remote)
runs-on: ubuntu-latest
env:
EXE: ./bin/colord
API_EXE: ./bin/api_example
ONT: ./test/M.bovis.fastq
ONT_LOSSY: ./test/M.bovis.fastq.quan
HIFI: ./test/D.melanogaster.fastq
HIFI_LOSSY: ./test/D.melanogaster.fastq.quan
CLR: ./test/A.thaliana.fastq
CLR_LOSSY: ./test/A.thaliana.fastq.quan
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v2
with:
submodules: recursive
- name: make
run: make -j2
- name: ONT default
run: |
$EXE compress-ont $ONT ont.default
$EXE decompress ont.default ont.default.fastq
cmp $ONT_LOSSY ont.default.fastq
- name: HiFi default
run: |
$EXE compress-pbhifi $HIFI hifi.default
$EXE decompress hifi.default hifi.default.fastq
cmp $HIFI_LOSSY hifi.default.fastq
- name: CLR default
run: |
$EXE compress-pbraw $CLR clr.default
$EXE decompress clr.default clr.default.fastq
cmp $CLR_LOSSY clr.default.fastq
- name: ONT lossless
run: |
$EXE compress-ont --qual org $ONT ont.lossless
$EXE decompress ont.lossless ont.lossless.fastq
cmp $ONT ont.lossless.fastq
- name: CLR lossless
run: |
$EXE compress-pbraw -q org $CLR clr.lossless
$EXE decompress clr.lossless clr.lossless.fastq
cmp $CLR clr.lossless.fastq
- name: HiFi balanced
run: |
$EXE compress-pbhifi --priority balanced $HIFI hifi.balanced
$EXE decompress hifi.balanced hifi.balanced.fastq
cmp $HIFI_LOSSY hifi.balanced.fastq
- name: CLR ratio
run: |
$EXE compress-pbraw --priority ratio $CLR clr.ratio
$EXE decompress clr.ratio clr.ratio.fastq
cmp $CLR_LOSSY clr.ratio.fastq
- name: ONT reference based
run: |
$EXE compress-ont -G ./test/M.bovis-reference.fna -s $ONT ont.refbased
$EXE decompress ont.refbased ont.refbased.fastq
cmp $ONT_LOSSY ont.refbased.fastq
- name: Archives information
run: |
$EXE info ont.default
$EXE info hifi.default
$EXE info clr.default
$EXE info ont.lossless
$EXE info hifi.balanced
$EXE info clr.ratio
- name: ONT default (API)
run: |
$API_EXE ont.default > ont.default.api
cmp $ONT_LOSSY ont.default.api
- name: HiFi balanced (API)
run: |
$API_EXE hifi.balanced > hifi.balanced.api
cmp $HIFI_LOSSY hifi.balanced.api
- name: ONT reference-based (API)
run: |
$API_EXE ont.refbased > ont.refbased.api
cmp $ONT_LOSSY ont.refbased.api
- name: CLR lossless (API)
run: |
$API_EXE clr.lossless > clr.lossless.api
cmp $CLR clr.lossless.api
macos-remote:
name: macOS build (remote)
runs-on: macOS-11
steps:
- name: Checkout repository and submodules
uses: actions/checkout@v2
with:
submodules: recursive
- name: make
run: make -j2