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fixup
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‎.github/workflows/ci.yml‎

Lines changed: 46 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -35,12 +35,17 @@ jobs:
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with:
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version: "${{ matrix.NXF_VER }}"
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -52,16 +57,16 @@ jobs:
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- name: Replace remote paths in samplesheets
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run: |
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for f in ./test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
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done;
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- name: Run pipeline with test data
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ./test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_salmon:
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name: Test STAR Salmon with workflow parameters
@@ -87,12 +92,17 @@ jobs:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: ${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -104,8 +114,8 @@ jobs:
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- name: Replace remote paths in samplesheets
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run: |
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for f in ./test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
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for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
@@ -118,7 +128,7 @@ jobs:
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- name: Run pipeline with STAR and various parameters
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run: |
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
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nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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star_rsem:
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name: Test STAR RSEM with workflow parameters
@@ -133,12 +143,17 @@ jobs:
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- name: Check out pipeline code
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uses: actions/checkout@v2
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- name: Hash Github Workspace
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id: hash_workspace
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run: |
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echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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- name: Cache test data
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id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
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key: rnaseq3_10-test-data
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key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
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- name: Check out test data
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if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -150,8 +165,8 @@ jobs:
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- name: Replace remote paths in samplesheets
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run: |
153-
for f in ./test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
168+
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
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sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
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cat $f
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echo "========================================"
@@ -164,7 +179,7 @@ jobs:
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- name: Run pipeline with RSEM STAR and various parameters
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run: |
167-
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
182+
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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hisat2:
170185
name: Test HISAT2 with workflow parameters
@@ -179,12 +194,17 @@ jobs:
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- name: Check out pipeline code
180195
uses: actions/checkout@v2
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197+
- name: Hash Github Workspace
198+
id: hash_workspace
199+
run: |
200+
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
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182202
- name: Cache test data
183203
id: cache-testdata
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uses: actions/cache@v3
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with:
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path: test-datasets/
187-
key: rnaseq3_10-test-data
207+
key: rnaseq-${{ steps.hash_workspace.outputs.digest }}
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189209
- name: Check out test data
190210
if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -196,8 +216,8 @@ jobs:
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- name: Replace remote paths in samplesheets
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run: |
199-
for f in ./test-datasets/samplesheet/v3.10/*.csv; do
200-
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
219+
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
220+
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
201221
echo "========== $f ============"
202222
cat $f
203223
echo "========================================"
@@ -210,7 +230,7 @@ jobs:
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- name: Run pipeline with HISAT2 and various parameters
212232
run: |
213-
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
233+
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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215235
salmon:
216236
name: Test Salmon with workflow parameters
@@ -225,12 +245,18 @@ jobs:
225245
- name: Check out pipeline code
226246
uses: actions/checkout@v2
227247

248+
- name: Hash Github Workspace
249+
id: hash_workspace
250+
run: |
251+
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
252+
253+
228254
- name: Cache test data
229255
id: cache-testdata
230256
uses: actions/cache@v3
231257
with:
232258
path: test-datasets/
233-
key: rnaseq3_10-test-data
259+
key: ${{ steps.hash_workspace.outputs.digest }}
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235261
- name: Check out test data
236262
if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -242,8 +268,8 @@ jobs:
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- name: Replace remote paths in samplesheets
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run: |
245-
for f in ./test-datasets/samplesheet/v3.10/*.csv; do
246-
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=./test-datasets/=g" $f
271+
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
272+
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
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echo "========== $f ============"
248274
cat $f
249275
echo "========================================"
@@ -256,4 +282,4 @@ jobs:
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- name: Run pipeline with Salmon and various parameters
258284
run: |
259-
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ./test-datasets/
285+
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/

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