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Cache data for GHA #933

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merged 12 commits into from
Jan 27, 2023
Merged

Cache data for GHA #933

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ea237f4
Add tests samplesheet in the main repo
maxulysse Jan 27, 2023
ba19814
add params.test_data_base
maxulysse Jan 27, 2023
f1941ae
this is why you should not edit JSON files
maxulysse Jan 27, 2023
e2e574a
trying to use local files
maxulysse Jan 27, 2023
2d8c44c
use samplesheet in the test_data repo
maxulysse Jan 27, 2023
0b4b19b
fix path
maxulysse Jan 27, 2023
423ba0b
fix path
maxulysse Jan 27, 2023
785ea73
fix path
maxulysse Jan 27, 2023
f9f467c
fix path
maxulysse Jan 27, 2023
bd4f148
uncache data
maxulysse Jan 27, 2023
8770ee6
re-cache data
maxulysse Jan 27, 2023
1c3dcc1
should not have updated the data that is cached...
maxulysse Jan 27, 2023
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130 changes: 125 additions & 5 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,33 @@ jobs:
with:
version: "${{ matrix.NXF_VER }}"

- name: Cache test data
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I could swear there was a way where we don't have to repeat this big block of code for every test?

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Probably, but we'll rewrote the tests soon enough, so we'll fix that in a future PR

id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: rnaseq3-test-data

- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: rnaseq3
path: test-datasets/

- name: Replace remote paths in samplesheets
run: |
for f in tests/csv/3.10/*csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_salmon:
name: Test STAR Salmon with workflow parameters
Expand All @@ -62,14 +86,38 @@ jobs:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: rnaseq3-test-data

- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: rnaseq3
path: test-datasets/

- name: Replace remote paths in samplesheets
run: |
for f in tests/csv/3.10/*csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;

- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

star_rsem:
name: Test STAR RSEM with workflow parameters
Expand All @@ -84,14 +132,38 @@ jobs:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: rnaseq3-test-data

- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: rnaseq3
path: test-datasets/

- name: Replace remote paths in samplesheets
run: |
for f in tests/csv/3.10/*csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;

- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with RSEM STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

hisat2:
name: Test HISAT2 with workflow parameters
Expand All @@ -106,14 +178,38 @@ jobs:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: rnaseq3-test-data

- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: rnaseq3
path: test-datasets/

- name: Replace remote paths in samplesheets
run: |
for f in tests/csv/3.10/*csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;

- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with HISAT2 and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

salmon:
name: Test Salmon with workflow parameters
Expand All @@ -128,11 +224,35 @@ jobs:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: rnaseq3-test-data

- name: Check out test data
if: steps.cache-testdata.outputs.cache-hit != 'true'
uses: actions/checkout@v3
with:
repository: nf-core/test-datasets
ref: rnaseq3
path: test-datasets/

- name: Replace remote paths in samplesheets
run: |
for f in tests/csv/3.10/*csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;

- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with Salmon and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
22 changes: 11 additions & 11 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -20,19 +20,19 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/v3.10/samplesheet_test.csv'
input = "${projectDir}/tests/csv/3.10/samplesheet_test.csv"

// Genome references
fasta = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fasta'
gtf = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz'
gff = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz'
transcript_fasta = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta'
additional_fasta = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz'

bbsplit_fasta_list = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/bbsplit_fasta_list.txt'
hisat2_index = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz'
salmon_index = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz'
rsem_index = 'https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz'
fasta = "${params.test_data_base}/reference/genome.fasta"
gtf = "${params.test_data_base}/reference/genes.gtf.gz"
gff = "${params.test_data_base}/reference/genes.gff.gz"
transcript_fasta = "${params.test_data_base}/reference/transcriptome.fasta"
additional_fasta = "${params.test_data_base}/reference/gfp.fa.gz"

bbsplit_fasta_list = "${params.test_data_base}/reference/bbsplit_fasta_list.txt"
hisat2_index = "${params.test_data_base}/reference/hisat2.tar.gz"
salmon_index = "${params.test_data_base}/reference/salmon.tar.gz"
rsem_index = "${params.test_data_base}/reference/rsem.tar.gz"

// Other parameters
skip_bbsplit = false
Expand Down
1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,7 @@ params {
config_profile_contact = null
config_profile_url = null
config_profile_name = null
test_data_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3'
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// Max resource options
// Defaults only, expecting to be overwritten
Expand Down
7 changes: 7 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -580,6 +580,13 @@
"description": "Institutional config URL link.",
"hidden": true,
"fa_icon": "fas fa-users-cog"
},
"test_data_base": {
"type": "string",
"default": "https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq3",
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Why rnaseq3 ?

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Created a subset of rnaseq which contains only the data actually used in the tests

"description": "Base path / URL for data used in the test profiles",
"help_text": "Warning: The `-profile test` samplesheet file itself contains remote paths. Setting this parameter does not alter the contents of that file.",
"hidden": true
}
}
},
Expand Down
8 changes: 8 additions & 0 deletions tests/csv/3.10/samplesheet_test.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
sample,fastq_1,fastq_2,strandedness
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WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357070_2.fastq.gz,auto
WT_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357071_2.fastq.gz,auto
WT_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357072_2.fastq.gz,reverse
RAP1_UNINDUCED_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357073_1.fastq.gz,,auto
RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357074_1.fastq.gz,,reverse
RAP1_UNINDUCED_REP2,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357075_1.fastq.gz,,reverse
RAP1_IAA_30M_REP1,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/testdata/GSE110004/SRR6357076_2.fastq.gz,reverse