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test.yaml
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name: Test Geneshot
on: [push, pull_request]
jobs:
complete_workflow:
runs-on: ubuntu-latest
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=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2,label1" --distance_threshold 0.5 -w work/ --eggnog_db false --eggnog_dmnd false --taxonomic_dmnd false -with-docker ubuntu:latest
- name: Rerun corncob
run: |
NXF_VER=20.04.1 nextflow run run_corncob.nf -c nextflow.config.sample -profile testing --input_hdf output/geneshot.results.hdf5 --input_folder output/ --output_folder output_label2 --output_prefix geneshot_label2 --formula "label2" -w work/ -with-docker ubuntu:latest
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
- name: Validate results (python 3.7)
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:py37 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
no_preprocessing:
runs-on: ubuntu-latest
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=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest --nopreprocess
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
add_formula:
runs-on: ubuntu-latest
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=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest
- name: Download annotations
run: |
wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog_proteins.dmnd && wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog.db
- name: Add annotations
run: |
NXF_VER=20.04.1 nextflow run run_annotations.nf -c nextflow.config.sample -profile testing --input_hdf output/geneshot.results.hdf5 --gene_fasta output/ref/genes.fasta.gz --output_folder output_with_annotations --output_hdf geneshot.results.hdf5 --eggnog_db eggnog.db --eggnog_dmnd eggnog_proteins.dmnd -w work/ -with-docker ubuntu:latest
- name: Run corncob
run: |
NXF_VER=20.04.1 nextflow run run_corncob.nf -c nextflow.config.sample -profile testing --input_hdf output_with_annotations/geneshot.results.hdf5 --input_folder output/ --output_folder output_with_corncob --output_prefix geneshot --formula "label1,label2" -w work/ -with-docker ubuntu:latest
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output_with_corncob/geneshot.label1_label2.corncob.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --check-corncob
no_assembly:
runs-on: ubuntu-latest
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=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.5 -w work/ --noannot -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly --check-corncob
eggnog:
runs-on: ubuntu-latest
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: Download annotations
run: |
wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog_proteins.dmnd && wget https://github.com/eggnogdb/eggnog-mapper/raw/master/tests/fixtures/eggnog.db
- name: Run geneshot
run: |
NXF_VER=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --formula "label1 + label2" --distance_threshold 0.15 -w work/ -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz --eggnog_dmnd eggnog_proteins.dmnd --eggnog_db eggnog.db --taxonomic_dmnd false
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly --check-corncob
composition:
runs-on: ubuntu-latest
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=20.04.1 nextflow run main.nf -c nextflow.config.sample -profile testing --manifest data/mock.manifest.csv --output output --hg_index data/hg_chr_21_bwa_index.tar.gz --distance_threshold 0.5 -w work/ -with-docker ubuntu:latest --gene_fasta data/genes.fasta.2.gz --composition --taxonomic_dmnd false --eggnog_db false --eggnog_dmnd false
- name: Validate results
run: |
docker run --rm -v $PWD:/share quay.io/fhcrc-microbiome/python-pandas:v1.0.3 python3 /share/bin/validate_geneshot_output.py --results-hdf /share/output/geneshot.results.hdf5 --details-hdf /share/output/geneshot.details.hdf5 --skip-assembly