From caefd94f0a460d0194570a9fa2e5d8c499139240 Mon Sep 17 00:00:00 2001 From: Foivos Gypas Date: Sun, 20 Oct 2024 23:09:15 +0200 Subject: [PATCH] Dockerfile, add docker test and update in samtools dependency --- .github/workflows/ci.yml | 35 +++- Dockerfile | 37 +++++ tests/input_files/config_docker.yaml | 18 +++ tests/input_files/samples_docker.tsv | 3 + .../expected_output.files | 151 ++++++++++++++++++ .../expected_output.md5 | 133 +++++++++++++++ .../test.local.sh | 51 ++++++ workflow/envs/samtools.yaml | 1 + 8 files changed, 426 insertions(+), 3 deletions(-) create mode 100644 Dockerfile create mode 100644 tests/input_files/config_docker.yaml create mode 100644 tests/input_files/samples_docker.tsv create mode 100644 tests/test_integration_workflow_with_docker/expected_output.files create mode 100644 tests/test_integration_workflow_with_docker/expected_output.md5 create mode 100755 tests/test_integration_workflow_with_docker/test.local.sh diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c52b72b..4b460b9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,9 +1,9 @@ name: CI on: - # push: - # branches: - # - '*' + push: + branches: + - '*' pull_request: branches: - main @@ -214,3 +214,32 @@ jobs: - name: Run SRA downloads workflow run: bash tests/test_sra_download_with_conda/test.local.sh + integration-docker: + needs: + - snakemake-graphs-format + runs-on: ubuntu-20.04 + defaults: + run: + shell: bash -l {0} + steps: + + - name: Checkout zarp repository + uses: actions/checkout@v4 + + - name: Setup miniconda & zarp env + uses: conda-incubator/setup-miniconda@v3 + with: + python-version: "3.10" + mamba-version: "*" + channels: conda-forge + channel-priority: true + auto-update-conda: false + activate-environment: zarp + environment-file: install/environment.yml + auto-activate-base: false + + - name: Update zarp env with dev. packages + run: mamba env update -p $CONDA_PREFIX -f install/environment.dev.yml + + - name: Run test script + run: bash tests/test_integration_workflow_with_docker/test.local.sh \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..33bd647 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,37 @@ +FROM continuumio/miniconda3:24.7.1-0 + + +COPY install/environment.yml /environment.yml +COPY workflow /workflow +COPY resources /resources +COPY tests/input_files/config.yaml /config.yaml +COPY tests/input_files/samples.tsv /samples.tsv +COPY tests/input_files/rule_config.yaml /rule_config.yaml +COPY tests/input_files/project1/synthetic.mate_1.fastq.gz /project1/synthetic.mate_1.fastq.gz +COPY tests/input_files/project1/synthetic.mate_2.fastq.gz /project1/synthetic.mate_2.fastq.gz +COPY tests/input_files/project2/synthetic.mate_1.fastq.gz /project2/synthetic.mate_1.fastq.gz +COPY tests/input_files/homo_sapiens/annotation.gtf /annotation.gtf +COPY tests/input_files/homo_sapiens/genome.fa /genome.fa + +RUN sed -i 's# - conda-forge##' workflow/envs/STAR.yaml && \ + sed -i 's#2.7.11#2.7.10#' workflow/envs/STAR.yaml && \ + sed -i 's#../input_files/project1/#/project1/#g' /samples.tsv && \ + sed -i 's#../input_files/project2/#/project2/#g' /samples.tsv && \ + sed -i 's#../input_files/homo_sapiens/##g' /samples.tsv && \ + sed -i 's#../input_files/##' /config.yaml + +RUN conda install -c conda-forge mamba --yes && \ + mamba env create -f /environment.yml && \ + conda clean --all --yes + +RUN echo "source activate zarp" > ~/.bashrc + +ENV SNAKEMAKE_CONDA_PREFIX="/conda_envs" +ENV PATH=/opt/conda/envs/zarp/bin:$PATH + +RUN snakemake -p --snakefile /workflow/Snakefile --configfile /config.yaml --cores 4 --use-conda --conda-create-envs-only --verbose && \ + conda clean --all --yes + +RUN rm /config.yaml /samples.tsv /rule_config.yaml /project1/synthetic.mate_1.fastq.gz /project1/synthetic.mate_2.fastq.gz /project2/synthetic.mate_1.fastq.gz + +RUN mkdir -p /data \ No newline at end of file diff --git a/tests/input_files/config_docker.yaml b/tests/input_files/config_docker.yaml new file mode 100644 index 0000000..d43470d --- /dev/null +++ b/tests/input_files/config_docker.yaml @@ -0,0 +1,18 @@ +--- + # Required fields + samples: "data/samples_docker.tsv" + output_dir: "data/results" + log_dir: "data/logs" + cluster_log_dir: "data/logs/cluster" + kallisto_indexes: "data/results/kallisto_indexes" + salmon_indexes: "data/results/salmon_indexes" + star_indexes: "data/results/star_indexes" + alfa_indexes: "data/results/alfa_indexes" + # Optional fields + rule_config: "data/rule_config.yaml" + report_description: "No description provided by user" + report_logo: "../../images/logo.128px.png" + report_url: "https://zavolan.biozentrum.unibas.ch/" + author_name: "NA" + author_email: "NA" +... diff --git a/tests/input_files/samples_docker.tsv b/tests/input_files/samples_docker.tsv new file mode 100644 index 0000000..f1c1ee7 --- /dev/null +++ b/tests/input_files/samples_docker.tsv @@ -0,0 +1,3 @@ +sample seqmode fq1 index_size kmer fq1_3p fq1_5p organism gtf genome sd mean libtype fq1_polya_3p fq1_polya_5p fq2 fq2_3p fq2_5p fq2_polya_3p fq2_polya_5p +synthetic_10_reads_paired_synthetic_10_reads_paired pe data/project1/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens data/annotation.gtf data/genome.fa 100 250 ISF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX data/project1/synthetic.mate_2.fastq.gz AGATCGGAAGAGCGT XXXXXXXXXXXXX XXXXXXXXXXXXXXXXX TTTTTTTTTTTTTTTTT +synthetic_10_reads_mate_1_synthetic_10_reads_mate_1 se data/project2/synthetic.mate_1.fastq.gz 75 31 AGATCGGAAGAGCACA XXXXXXXXXXXXX homo_sapiens data/annotation.gtf data/genome.fa 100 250 SF AAAAAAAAAAAAAAAAA XXXXXXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX XXXXXXXXXXXXX diff --git a/tests/test_integration_workflow_with_docker/expected_output.files b/tests/test_integration_workflow_with_docker/expected_output.files new file mode 100644 index 0000000..a64b5e3 --- /dev/null +++ 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+data/results/star_indexes/homo_sapiens/75/STAR_index/SAindex +data/results/star_indexes/homo_sapiens/75/STAR_index/sjdbInfo.txt +data/results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.fromGTF.out.tab +data/results/star_indexes/homo_sapiens/75/STAR_index/sjdbList.out.tab +data/results/star_indexes/homo_sapiens/75/STAR_index/transcriptInfo.tab +data/results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_adapters.fastq +data/results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq1.pe.remove_polya.fastq +data/results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_adapters.fastq 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+3ebe15878142b0967f366956e5e6120d data/results/homo_sapiens/samples/synthetic_10_reads_paired_synthetic_10_reads_paired/fastqc_trimmed/fq2_pe/synthetic_10_reads_paired_synthetic_10_reads_paired.fq2.pe.remove_polya_fastqc/Images/sequence_length_distribution.png diff --git a/tests/test_integration_workflow_with_docker/test.local.sh b/tests/test_integration_workflow_with_docker/test.local.sh new file mode 100755 index 0000000..2529238 --- /dev/null +++ b/tests/test_integration_workflow_with_docker/test.local.sh @@ -0,0 +1,51 @@ +#!/bin/bash + +# Tear down test environment +cleanup () { + rc=$? + rm -rf .cache/ + rm -rf .config/ + rm -rf .fontconfig/ + rm -rf .java/ + rm -rf .snakemake/ + rm -rf data/ + cd $user_dir + echo "Exit status: $rc" +} +trap cleanup EXIT + +# Set up test environment +set -eo pipefail # ensures that script exits at first command that exits with non-zero status +set -u # ensures that script exits when unset variables are used +set -x # facilitates debugging by printing out executed commands +user_dir=$PWD +script_dir="$(cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1 && pwd)" +cd $script_dir + +mkdir -p data +cp ../../tests/input_files/homo_sapiens/genome.fa data/genome.fa +cp ../../tests/input_files/homo_sapiens/annotation.gtf data/annotation.gtf +cp -r ../../tests/input_files/project1 data/project1 +cp -r ../../tests/input_files/project2 data/project2 +cp -r ../../tests/input_files/config_docker.yaml data/config_docker.yaml +cp ../../tests/input_files/rule_config.yaml data/rule_config.yaml +cp ../../tests/input_files/samples_docker.tsv data/samples_docker.tsv + +# Pull the zarp container +docker pull zavolab/zarp:1.0.0-rc.1 + +# Run tests with Docker +docker run \ + --platform linux/x86_64 \ + --mount type=bind,source=$script_dir/data,target=/data \ + -it zavolab/zarp:1.0.0-rc.1 \ + snakemake \ + -p \ + --snakefile /workflow/Snakefile \ + --configfile data/config_docker.yaml \ + --cores 4 --use-conda --verbose + +# Check md5 sum of some output files +find data/results/ -type f -name \*\.gz -exec gunzip '{}' \; +find data/results/homo_sapiens/ -type f -name \*\.zip -exec sh -c 'unzip -o {} -d $(dirname {})' \; +md5sum --check "expected_output.md5" \ No newline at end of file diff --git a/workflow/envs/samtools.yaml b/workflow/envs/samtools.yaml index e1478a1..b41941a 100644 --- a/workflow/envs/samtools.yaml +++ b/workflow/envs/samtools.yaml @@ -1,5 +1,6 @@ --- channels: + - conda-forge - bioconda dependencies: - samtools=1.19.2