diff --git a/CHANGELOG.md b/CHANGELOG.md index 184193b..8f6e8a8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -24,6 +24,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), - `--offline` renamed to `--airplane` - Improved warnings and error messages - Pins Bowtie2>=2.5.4 and Minimap2>=2.28 +- Removed space before `/1` and `/2` when writing paired FASTQ @@ -51,7 +52,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), - Verification of downloaded index checksums in `manifest.json`. (#20) - Adds `version`, `aligner`, and `options` fields to log output. -### Fixed +### Changed - Prevents corruption of empty `fastq.gz` files when no reads remain after decontamination. (#24) @@ -78,7 +79,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), ## [0.2.0] - 2023-11-10 -### Improved +### Changed - Performance improvements for Illumina reads / Bowtie. - Added a space before `/1` and `/2` when renaming Illumina reads (with `--rename`), enhancing compatibility. - Improved logging. @@ -87,20 +88,6 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), ## [0.1.0] - 2023-07-23 -### Fixed +### Changed - Addressed issues #10, #19, #20, #22, #23, and #25. - Added extensive new tests. - - - -## [0.0.3] - 2023-07-20 - -### Updated -- Enhanced docstrings and updated the README. - - - -## [0.0.2] - 2023-07-20 - -### Documentation -- Initial README update. diff --git a/src/hostile/util.py b/src/hostile/util.py index 765c18b..4ceca32 100644 --- a/src/hostile/util.py +++ b/src/hostile/util.py @@ -86,7 +86,9 @@ def handle_alignment_exceptions(exception: subprocess.CalledProcessError) -> Non alignment_successful = False stream_empty = False if "function mm_idx_load": # Minimap2 index corruption - raise RuntimeError("Minimap2 index appears corrupted, run hostile index purge") + raise RuntimeError( + "Minimap2 index may be corrupted, run hostile index delete --mmi" + ) if "Error, fewer reads in file specified" in exception.stderr: # Bowtie2 raise RuntimeError("fastq1 and fastq2 contain different numbers of reads") if 'Failed to read header for "-"' in exception.stderr: