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Fix merge conflicts
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@drpatelh
drpatelh committed Oct 11, 2023
2 parents 8548006 + 1ff095a commit 6ca440c
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39 changes: 0 additions & 39 deletions .github/workflows/awsfulltest.yml
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33 changes: 0 additions & 33 deletions .github/workflows/awstest.yml
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250 changes: 246 additions & 4 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -35,9 +35,251 @@ jobs:
with:
version: "${{ matrix.NXF_VER }}"

- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}

- 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 ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f
echo "========== $f ============"
cat $f
echo "========================================"
done;
- name: Run pipeline with test data
# TODO nf-core: You can customise CI pipeline run tests as required
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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"
- "--gtf false"
- "--star_index false"
- "--transcript_fasta false"
- "--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@v2

- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}

- 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 ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ 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_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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"
- "--rsem_index false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}

- 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 ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ 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_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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"
- "--hisat2_index false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}

- 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 ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ 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_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
salmon:
name: Test 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_alignment --skip_pseudo_alignment"
- "--salmon_index false --transcript_fasta false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
- name: Cache test data
id: cache-testdata
uses: actions/cache@v3
with:
path: test-datasets/
key: ${{ steps.hash_workspace.outputs.digest }}

- 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 ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ 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_cache,docker --pseudo_aligner salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/
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