Create citation.cff #194
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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@v2 | |
| with: | |
| activate-environment: dragonflye | |
| auto-activate-base: false | |
| - name: Setup dragonflye Environment | |
| run: | | |
| conda install -y -c conda-forge -c bioconda mamba 'python=3.8.0' | |
| mamba 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 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 | |
| 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 |