diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 83e0d32..98c9ee1 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -49,6 +49,6 @@ jobs: shell: bash -l {0} run: just test-ci - name: Upload coverage reports to Codecov - uses: codecov/codecov-action@v3 + uses: codecov/codecov-action@v4 diff --git a/.github/workflows/draft-pdf.yml b/.github/workflows/draft-pdf.yml deleted file mode 100644 index f85b711..0000000 --- a/.github/workflows/draft-pdf.yml +++ /dev/null @@ -1,23 +0,0 @@ -on: [push] - -jobs: - paper: - runs-on: ubuntu-latest - name: Paper Draft - steps: - - name: Checkout - uses: actions/checkout@v3 - - name: Build draft PDF - uses: openjournals/openjournals-draft-action@master - with: - journal: joss - # This should be the path to the paper within your repo. - paper-path: paper/paper.md - - name: Upload - uses: actions/upload-artifact@v1 - with: - name: paper - # This is the output path where Pandoc will write the compiled - # PDF. Note, this should be the same directory as the input - # paper.md - path: paper/paper.pdf diff --git a/pyproject.toml b/pyproject.toml index 66abbed..2ff2e20 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "dnaapler" -version = "0.8.0" # change VERSION too +version = "0.8.1" # change VERSION too description = "Reorients assembled microbial sequences" authors = ["George Bouras "] license = "MIT" diff --git a/src/dnaapler/__init__.py b/src/dnaapler/__init__.py index 7de1f4c..ef60096 100755 --- a/src/dnaapler/__init__.py +++ b/src/dnaapler/__init__.py @@ -905,6 +905,18 @@ def all( gene = "repA,terL" elif db == "cog1474": gene = "cog1474" + elif db == "dnaA,cog1474": + gene = "dnaA,cog1474" + elif db == "cog1474,terl": + gene = "cog1474,terL" + elif db == "repa,cog1474": + gene = "repA,cog1474" + elif db == "dnaa,repa,cog1474": + gene = "dnaa,repa,cog1474" + elif db == "dnaa,terl,cog1474": + gene = "dnaa,terl,cog1474" + elif db == "repa,terl,cog1474": + gene = "repa,terl,cog1474" # custom if custom_db != "": diff --git a/src/dnaapler/utils/VERSION b/src/dnaapler/utils/VERSION index 8adc70f..c18d72b 100644 --- a/src/dnaapler/utils/VERSION +++ b/src/dnaapler/utils/VERSION @@ -1 +1 @@ -0.8.0 \ No newline at end of file +0.8.1 \ No newline at end of file diff --git a/src/dnaapler/utils/validation.py b/src/dnaapler/utils/validation.py index f221f8b..bf88f22 100644 --- a/src/dnaapler/utils/validation.py +++ b/src/dnaapler/utils/validation.py @@ -218,7 +218,22 @@ def validate_choice_db(ctx, param, value): """ checks the click.Choice option for the mode flag in bulk subcommand """ - choices = ["all", "dnaa", "repa", "terl", "dnaa,repa", "dnaa,terl", "repa,terl"] + choices = [ + "all", + "dnaa", + "repa", + "terl", + "dnaa,repa", + "dnaa,terl", + "repa,terl", + "cog1474", + "dnaA,cog1474", + "cog1474,terl", + "repa,cog1474", + "dnaa,repa,cog1474", + "dnaa,terl,cog1474", + "repa,terl,cog1474", + ] if value not in choices: raise click.BadParameter(f"Invalid choice. Choose from {', '.join(choices)}") return value diff --git a/tests/test_overall.py b/tests/test_overall.py index 1b74e4a..a5b6eec 100755 --- a/tests/test_overall.py +++ b/tests/test_overall.py @@ -246,6 +246,18 @@ def test_all_dnaa_repa(tmp_dir): exec_command(cmd) +""" +this one is for hybracter +""" + + +def test_all_dnaa_repa_cog1474(tmp_dir): + """test all dnaa repa cog1474 - for hybracter""" + input_fasta: Path = f"{overall_test_data}/all_test.fasta" + cmd = f"dnaapler all -i {input_fasta} -o {tmp_dir} -t 1 -f --db dnaa,repa,cog1474" + exec_command(cmd) + + def test_all_dnaa_terl(tmp_dir): """test all dnaa terl""" input_fasta: Path = f"{overall_test_data}/all_reorient_and_no_reorient.fasta"