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Simple pipeline level nf-tests #1272
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c49f446
Add direct replacements for existing tests
adamrtalbot 4d9acbb
Reorganised into discrete folders
adamrtalbot 08e89eb
More all tests into subdirectory for more organisation
adamrtalbot 967563b
remove redundant tests
adamrtalbot c2861cc
Remove invalid dependencies from GHA confirm-pass
adamrtalbot c00917c
Correct pipeline test path
adamrtalbot 622d8c6
Relative path AGAIN
adamrtalbot fe8673b
Merge branch 'dev' into pipeline_level_tests_simple
adamrtalbot bcc1a00
Merge branch 'dev' into pipeline_level_tests_simple
adamrtalbot e01e195
Remove r-base from software versions
adamrtalbot 6e6a254
Move repo tests config to tests/config
adamrtalbot 76473d2
Add test config
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|
@@ -19,73 +19,6 @@ concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | ||
cancel-in-progress: true | ||
jobs: | ||
star_salmon: | ||
name: Test STAR Salmon with workflow parameters | ||
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: | ||
- "--skip_qc" | ||
- "--skip_trimming" | ||
- "--min_mapped_reads 90" | ||
- "--with_umi" | ||
- "--with_umi --skip_trimming" | ||
- "--remove_ribo_rna --skip_qualimap" | ||
- "--bam_csi_index" | ||
- "--save_align_intermeds --save_reference" | ||
- "--featurecounts_group_type false" | ||
- "--trimmer fastp" | ||
|
||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v4 | ||
|
||
- name: Setup Nextflow | ||
uses: nf-core/[email protected] | ||
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||
- name: Run pipeline with STAR and various parameters | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results | ||
|
||
star_rsem: | ||
name: Test STAR RSEM with workflow parameters | ||
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: | ||
- "--skip_qc" | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v4 | ||
|
||
- name: Setup Nextflow | ||
uses: nf-core/[email protected] | ||
|
||
- name: Run pipeline with RSEM STAR and various parameters | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results | ||
|
||
hisat2: | ||
name: Test HISAT2 with workflow parameters | ||
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | ||
runs-on: ubuntu-latest | ||
strategy: | ||
matrix: | ||
parameters: | ||
- "--skip_qc" | ||
steps: | ||
- name: Check out pipeline code | ||
uses: actions/checkout@v4 | ||
|
||
- name: Setup Nextflow | ||
uses: nf-core/[email protected] | ||
|
||
- name: Run pipeline with HISAT2 and various parameters | ||
run: | | ||
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results | ||
|
||
pseudo: | ||
name: Test Pseudoaligners with workflow parameters | ||
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | ||
|
@@ -244,7 +177,7 @@ jobs: | |
|
||
confirm-pass: | ||
runs-on: ubuntu-latest | ||
needs: [test, star_salmon, star_rsem, hisat2, pseudo] | ||
needs: [test, pseudo] | ||
if: always() | ||
steps: | ||
- name: All tests ok | ||
|
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@@ -0,0 +1,22 @@ | ||
nextflow_pipeline { | ||
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||
name "Test pipeline" | ||
script "../../../main.nf" | ||
tag "rnaseq" | ||
tag "PIPELINE" | ||
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||
test("--featurecounts_group_type false") { | ||
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when { | ||
params { | ||
outdir = "$outputDir" | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' | ||
featurecounts_group_type = false | ||
} | ||
} | ||
|
||
then { | ||
assert workflow.success | ||
} | ||
} | ||
} |
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nextflow_pipeline { | ||
|
||
name "Test pipeline" | ||
script "../../../main.nf" | ||
tag "rnaseq" | ||
tag "PIPELINE" | ||
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test("--min_mapped_reads 90") { | ||
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when { | ||
params { | ||
outdir = "$outputDir" | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' | ||
min_mapped_reads = 90 | ||
} | ||
} | ||
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||
then { | ||
assert workflow.success | ||
} | ||
} | ||
} |
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nextflow_pipeline { | ||
|
||
name "Test pipeline" | ||
script "../../../main.nf" | ||
tag "rnaseq" | ||
tag "PIPELINE" | ||
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test("--remove_ribo_rna") { | ||
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||
when { | ||
params { | ||
outdir = "$outputDir" | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' | ||
remove_ribo_rna = true | ||
} | ||
} | ||
|
||
then { | ||
assert workflow.success | ||
} | ||
} | ||
} |
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---|---|---|
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nextflow_pipeline { | ||
|
||
name "Test pipeline" | ||
script "../../../main.nf" | ||
tag "rnaseq" | ||
tag "PIPELINE" | ||
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test("--skip_qc") { | ||
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when { | ||
params { | ||
outdir = "$outputDir" | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' | ||
skip_qc = true | ||
} | ||
} | ||
|
||
then { | ||
assert workflow.success | ||
} | ||
} | ||
} |
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---|---|---|
@@ -0,0 +1,22 @@ | ||
nextflow_pipeline { | ||
|
||
name "Test pipeline" | ||
script "../../../main.nf" | ||
tag "rnaseq" | ||
tag "PIPELINE" | ||
|
||
test("--skip_trimming") { | ||
|
||
when { | ||
params { | ||
outdir = "$outputDir" | ||
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/samplesheet/v3.10/samplesheet_test.csv' | ||
skip_qc = true | ||
} | ||
} | ||
|
||
then { | ||
assert workflow.success | ||
} | ||
} | ||
} |
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tests/tests/default/
?why not
tests/default/
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The reason is to keep it tidy. You have a primary
tests/
folder withtests
,lib
and other stuff (e.g.conf
).Without it, you would end up with this which I think is messy:
But I could be convinced otherwise.
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We could move the
tests/nextflow.config
file intotests/config/nextflow.config
for consistency?There was a problem hiding this comment.
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I'd go with:
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Oh bother automerge was too quick.