Skip to content

Kallisto quantification #1970

Kallisto quantification

Kallisto quantification #1970

Workflow file for this run

name: nf-core CI
# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
env:
NXF_ANSI_LOG: false
concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true
jobs:
test:
name: Run pipeline with test data
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ 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
run: |
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/
pseudo:
name: Test Pseudoaligners with workflow parameters
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--pseudo_aligner salmon --skip_qc"
- "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment"
- "--pseudo_aligner salmon --salmon_index false --transcript_fasta false"
- "--pseudo_aligner kallisto --skip_qc"
- "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment"
- "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
- name: Hash Github Workspace
id: hash_workspace
run: |
echo "digest=$(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 or Kallisto and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/