start a conversion to python #204
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| name: dragonflye-test | |
| on: | |
| push: | |
| branches: [ main, dev ] | |
| pull_request: | |
| branches: [ main, dev ] | |
| jobs: | |
| dragonflye-tests: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - name: Checkout rpetit3/dragonflye | |
| uses: actions/checkout@v2 | |
| - name: Checkout bactopia/bactopia-tests repo | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: bactopia/bactopia-tests | |
| path: bactopia-tests | |
| - name: Setup miniconda | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| activate-environment: dragonflye | |
| auto-activate-base: false | |
| miniforge-version: latest | |
| - name: Setup dragonflye Environment | |
| run: | | |
| conda install -y -c conda-forge -c bioconda 'assembly-scan>=0.4.0' any2fasta bwa dnaapler fastp flye 'kmc>=3.1' 'medaka>=1.11.0' miniasm 'nanoq>=0.8.1' perl perl-file-spec perl-findbin 'polypolish>=0.6.0' pilon pigz racon 'rasusa>=1' raven-assembler samtools samclip seqtk porechop | |
| - name: Environment Information | |
| run: uname -a && env | |
| - name: Test dragonflye basics | |
| run: | | |
| echo "Testing dragonflye" | |
| bin/dragonflye --version | |
| bin/dragonflye --help | |
| - name: Test Raven Assembler (quality filtered) | |
| run: | | |
| echo "Test Raven Assembler (quality filtered)" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --prefix ERR3772599 --cpus 0 --nopolish --outdir tests/raven-minquality --gsize 300000 --assembler raven --minquality 8 | |
| - name: Test Raven Assembler (quality filtered, no length filter) | |
| run: | | |
| echo "Test Raven Assembler (quality filtered, no length filter)" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir tests/raven-minquality-nominreadlen --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 | |
| - name: Test Raven Assembler (quality filtered, no length filter, trimming) | |
| run: | | |
| echo "Test Raven Assembler (quality filtered, no length filter)" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir tests/raven-minquality-nominreadlen-trim --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 --trim | |
| - name: Test Raven Assembler (quality filtered, no length filter, trimming, trim opts) | |
| run: | | |
| echo "Test Raven Assembler (quality filtered, no length filter)" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir tests/raven-minquality-nominreadlen-trimopts --gsize 300000 --assembler raven --minquality 6 --minreadlen 0 --trim --trimopts '--adapter_threshold 95' | |
| - name: Test Raven Assembler + Rasusa Depth Filter | |
| run: | | |
| echo "Testing Raven Assembler" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --prefix ERR3772599-raven --cpus 0 --nopolish --depth 5 --outdir tests/raven --gsize 300000 --assembler raven | |
| - name: Test Raven Assembler + Racon Polish | |
| run: | | |
| echo "Testing Raven Assembler + Racon Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-racon --gsize 300000 --assembler raven | |
| - name: Test Raven Assembler + Medaka Polish | |
| run: | | |
| echo "Testing Flye Assembler + Medaka Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-medaka --gsize 300000 --assembler raven --racon 0 --model r103_min_high_g345 | |
| - name: Test Raven Assembler + Medaka Polish + --medaka_opts | |
| run: | | |
| echo "Testing Flye Assembler + Medaka Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-medaka-opts --gsize 300000 --assembler raven --racon 0 --model r103_min_high_g345 --medaka_opts '-b 200' | |
| - name: Test Raven Assembler + Racon & Medaka Polish | |
| run: | | |
| echo "Testing Flye Assembler + Racon & Medaka Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-both --gsize 300000 --assembler raven | |
| - name: Test Raven Assembler + Racon & Polypolish Polish | |
| run: | | |
| echo "Testing Raven Assembler + Racon & Polypolish Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --R1 bactopia-tests/data/species/portiera/illumina/SRR2838702_R1.fastq.gz --R2 bactopia-tests/data/species/portiera/illumina/SRR2838702_R2.fastq.gz --cpus 0 --outdir tests/raven-polypolish --gsize 300000 --assembler raven | |
| - name: Test Raven Assembler + Racon & Polypolish Careful Polish | |
| run: | | |
| echo "Testing Raven Assembler + Racon & Polypolish Careful Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --R1 bactopia-tests/data/species/portiera/illumina/SRR2838702_R1.fastq.gz --R2 bactopia-tests/data/species/portiera/illumina/SRR2838702_R2.fastq.gz --cpus 0 --outdir tests/raven-polypolish-careful --gsize 300000 --assembler raven --polypolish_careful | |
| - name: Test Raven Assembler + Racon & Pilon Polish | |
| run: | | |
| echo "Testing Raven Assembler + Racon & Pilon Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --R1 bactopia-tests/data/species/portiera/illumina/SRR2838702_R1.fastq.gz --R2 bactopia-tests/data/species/portiera/illumina/SRR2838702_R2.fastq.gz --cpus 0 --outdir tests/raven-pilon --gsize 300000 --assembler raven --polypolish 0 --pilon 1 | |
| - name: Test Miniasm Assembler | |
| run: | | |
| echo "Testing Miniasm Assembler" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --prefix ERR3772599_mini.asm --cpus 1 --nopolish --outdir tests/miniasm --gsize 300000 --assembler miniasm | |
| - name: Test Flye Assembler | |
| run: | | |
| echo "Testing Flye Assembler" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --nopolish --outdir tests/flye --gsize 300000 --assembler flye | |
| - name: Test Flye Assembler (nanohq) | |
| run: | | |
| echo "Testing Flye Assembler (with --nano-hq)" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --prefix ERR3772599-nano.hq --cpus 0 --nopolish --outdir tests/flyehq --gsize 300000 --assembler flye --nanohq | |
| - name: Test --list_models | |
| run: | | |
| echo "Testing --list_models" | |
| bin/dragonflye --list_models 2>&1 | grep r1041_e82_400bps_sup_variant_v4.2.0 | |
| - name: Test Raven Assembler + Medaka Polish + Model version dots | |
| run: | | |
| echo "Testing Raven Assembler + Medaka Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-medaka-version-dots --gsize 300000 --assembler raven --racon 0 --model r1041_e82_400bps_sup_variant_v4.2.0 | |
| - name: Test Raven Assembler + Medaka Polish + Model r1041_e82_400bps_sup_g615 | |
| run: | | |
| echo "Testing Raven Assembler + Medaka Polish" | |
| bin/dragonflye --reads bactopia-tests/data/species/portiera/nanopore/ERR3772599.fastq.gz --cpus 0 --outdir tests/raven-medaka-version-g615 --gsize 300000 --assembler raven --racon 0 --model r1041_e82_400bps_sup_g615 |