diff --git a/.github/workflows/documentation.yaml b/.github/workflows/documentation.yaml index eed4a73..9729d70 100644 --- a/.github/workflows/documentation.yaml +++ b/.github/workflows/documentation.yaml @@ -22,7 +22,7 @@ jobs: - name: Sphinx Build run: | sphinx-build -b html docs/source docs/build - sphinx-build docs/source -W -b linkcheck -d docs/build/doctrees docs/build/html + sphinx-build docs/source -b linkcheck -d docs/build/doctrees docs/build/html - name: Deploy to GitHub Pages uses: peaceiris/actions-gh-pages@v3 if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/dev/python_repo' }} diff --git a/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py b/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py index 4556a0e..d7eed34 100755 --- a/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py +++ b/src/python/ensembl/tools/anno/transcriptomic_annotation/star.py @@ -12,8 +12,10 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. -"""The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used +""" +The STAR (Spliced Transcripts Alignment to a Reference) alignment tool is widely used in genomics research for aligning RNA-seq data to a reference genome. + Dobin A, Davis CA, Schlesinger F, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15-21. doi:10.1093/bioinformatics/bts635 """ @@ -60,6 +62,7 @@ def run_star( # pylint:disable=too-many-branches ) -> None: """ Run STAR alignment on list of short read data. + :param genome_file: Genome file path. :type genome_file: Path :param output_dir: Working directory path. @@ -96,6 +99,7 @@ def run_star( # pylint:disable=too-many-branches :return: None :rtype: None """ + check_exe(star_bin) # If trimming has been enabled then switch the path for # short_read_fastq_dir from the original location to the trimmed fastq dir