STARsolo/.github/workflows/test.yml at main · cellgeni/STARsolo · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
name: "Test Workflow"
on:
    push:
        branches: [main, dev]
        paths-ignore:
            - 'data/whitelists.tar.gz'
            - 'README.md'
            - 'LICENSE'
            - 'scripts/**'
            - 'Dockerfile'
    pull_request:
        branches: [main, dev]

jobs:
    test:
        runs-on: ubuntu-latest
        container: quay.io/cellgeni/starsolo:base
        strategy:
            fail-fast: false
            matrix:
                case: [10x, 10x5p, dropseq, dropseq_bam, rhapsody, indrops, strt, smartseq]
        name: "Run tests for ${{ matrix.case }}"

        steps:
            - name: Checkout repository
              uses: actions/checkout@v5

            - name: Unpack test data
              run: tar -xzf data/test.tar.gz

            - name: Run starsolo and check against the truth set
              run: bash tests/test_platforms.sh ${{ matrix.case }}

    unit:
        runs-on: ubuntu-latest
        container: quay.io/cellgeni/starsolo:base
        name: "Run library and 10x recovery tests"

        steps:
            - name: Checkout repository
              uses: actions/checkout@v5

            - name: Unpack test data
              run: tar -xzf data/test.tar.gz

            - name: Library tests
              run: bash tests/test_lib.sh

            - name: 10x Velocyto and crash-recovery tests
              run: bash tests/test_recovery.sh

            - name: 10x with BAM, unmapped reads and overridden flags
              run: |
                set -e
                bin/starsolo 10x data/test/fastqs/10x 10x \
                    --ref data/test/reference/index \
                    --whitelist-dir data/test/whitelists \
                    --bam \
                    --cpus 2 \
                    -- --outReadsUnmapped Fastx --outFilterScoreMin 20 \
                       --limitBAMsortRAM 2000000000 --soloFeatures Gene GeneFull SJ Velocyto
                test -s 10x/Aligned.sortedByCoord.out.bam.bai
                bzip2 -t 10x/Unmapped.out.mate1.bz2
                test -d 10x/output/SJ