Corrected help message #617
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name: Test Geneshot | |
on: [push, pull_request] | |
jobs: | |
full: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run preprocess | |
run: | | |
NXF_VER=23.10.0 nextflow run main.nf --manifest data/mock.manifest.csv --output output --savereads --host_index data/hg_chr_21_bwa_index.tar.gz -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/qc/manifest.qc.csv ]] | |
[[ -s output/qc/Mock__11.R1.fastq.gz ]] | |
[[ -s output/qc/Mock__13__R1.noadapt.nohuman.fq.gz ]] | |
[[ -s output/MetaPhlAn2/metaphlan2.results.csv.gz ]] | |
[[ -s output/MetaPhlAn2/metaphlan2.species.h5ad ]] | |
[[ -s output/alleles/allele_info.csv.gz ]] | |
[[ -s output/alleles/alleles.faa.gz ]] | |
[[ -s output/alleles/alleles.faa.gz.dmnd ]] | |
[[ -s output/alleles/Allele_Cluster_info.csv.gz ]] | |
[[ -s output/alleles/centroids.C100.fastp.gz ]] | |
[[ -s output/alleles/centroids.C90.fastp.gz ]] | |
[[ -s output/alleles/centroids.C50.fastp.gz ]] | |
[[ -s output/alleles/centroids.C100.fastp.gz.dmnd ]] | |
[[ -s output/alleles/centroids.C90.fastp.gz.dmnd ]] | |
[[ -s output/alleles/centroids.C50.fastp.gz.dmnd ]] | |
[[ -s output/quantify/specimen_allele_quantity.h5ad ]] | |
preproccessing: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run preprocess | |
run: | | |
NXF_VER=23.10.0 nextflow run modules/preprocess.nf --manifest data/mock.manifest.csv --output output --host_index data/hg_chr_21_bwa_index.tar.gz -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/qc/manifest.qc.csv ]] | |
[[ -s output/qc/Mock__11.R1.fastq.gz ]] | |
[[ -s output/qc/Mock__13__R1.noadapt.nohuman.fq.gz ]] | |
composition_metaphlan2: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run geneshot | |
run: | | |
NXF_VER=23.10.0 nextflow run modules/composition.nf --manifest data/example_output/qc/manifest.qc.se.csv --output output -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/MetaPhlAn2/metaphlan2.results.csv.gz ]] | |
[[ -s output/MetaPhlAn2/metaphlan2.species.h5ad ]] | |
allele_catalog: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run geneshot | |
run: | | |
NXF_VER=23.10.0 nextflow run modules/allele_catalog.nf --manifest data/example_output/qc/manifest.qc.csv --output output -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/alleles/allele_info.csv.gz ]] | |
[[ -s output/alleles/alleles.faa.gz ]] | |
[[ -s output/alleles/alleles.faa.gz.dmnd ]] | |
allele_clustering: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run geneshot | |
run: | | |
NXF_VER=23.10.0 nextflow run modules/allele_clustering.nf --alleles data/example_output/alleles/alleles.faa.gz --allele_info data/example_output/alleles/allele_info.csv.gz --output output -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/alleles/Allele_Cluster_info.csv.gz ]] | |
[[ -s output/alleles/centroids.C100.fastp.gz ]] | |
[[ -s output/alleles/centroids.C90.fastp.gz ]] | |
[[ -s output/alleles/centroids.C50.fastp.gz ]] | |
[[ -s output/alleles/centroids.C100.fastp.gz.dmnd ]] | |
[[ -s output/alleles/centroids.C90.fastp.gz.dmnd ]] | |
[[ -s output/alleles/centroids.C50.fastp.gz.dmnd ]] | |
allele_quantification: | |
runs-on: ubuntu-22.04 | |
env: | |
NXF_ANSI_LOG: 0 | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Free disk space | |
run: | | |
sudo swapoff -a | |
sudo rm -f /swapfile | |
sudo apt clean | |
docker rmi $(docker image ls -aq) | |
df -h | |
- name: Run geneshot | |
run: | | |
NXF_VER=23.10.0 nextflow run modules/quantify.nf --manifest data/example_output/qc/manifest.qc.csv --allele_fasta data/example_output/alleles/alleles.faa.gz --output output -w work/ -with-docker ubuntu:22.04 -c nextflow.config.sample -profile testing | |
- name: Validate results | |
run: | | |
tree output/ | |
[[ -s output/quantify/specimen_allele_quantity.h5ad ]] |