irma-core - IRMA-core v0.6.0

Release Notes for v0.6.0 - 2025-08-29

Added

• Adds a new standalone process called sampler that provides support for randomly downsampling FastQ or FASTA files. Deinterleaving is also supported.

Changed

• Use threads and anonymous pipes (in Rust) when decompressing zipped inputs
• Improve error messages to include file names in trimmer and preprocess
• Other dependencies updated, such as a faster foldhash.

Fixes

• mergeSAMpairs: updated Zoe dependency (in v0.0.19, using v0.0.20) fixes hard clipping in merged reads. Reader error messages are also improved generally.

- Rust
Published by github-actions[bot] 6 months ago

irma-core - IRMA-core v0.5.1

Release Notes for v0.5.1 - 2025-06-03

Fixes

• Fixes a bug where --polyg-trim would trim the sequence but not the quality scores.

- Rust
Published by github-actions[bot] 9 months ago

irma-core - v0.5.0

Release Notes for v0.5.0 - 2025-05-30

Added

• preprocess (formerly qc-trim-deflate) now supports zipped inputs (fastq.gz files).

Changed

• Re-factor and specify dependencies.
• The process qc-trim-deflate is now called preprocess, and it includes most of the same functionality as trimmer (note that its arguments have been conformed to match trimmer rather than the legacy fastq_converter process).
• The deprecated fastq_converter will be removed in the next version.
• For trimmer/preprocess, --filter-widows can no longer be specified when there is only a single input file.
• For fastq_converter/preprocess, --keep-header has been removed since IRMA has made this an unmodifiable default since v1.1.2.

- Rust
Published by github-actions[bot] 9 months ago

irma-core - v0.4.3

Release Notes for v0.4.3 - 2025-05-01

Fixes

• Fixed bug in trimmer to allow handling of multi-member fastq.gz files

- Rust
Published by github-actions[bot] 10 months ago

irma-core - v0.4.2

Release Notes for v0.4.2 - 2025-04-30

Changed

• The Dockerfile has been updated for nextflow compatibility (it currently needed: awk, grep, ps, sed)
• The num-procs process now allows LOCAL_PROCS_OVERRIDE to be greater than the available cores. Use IFX_LOCAL_PROCS if you would like it capped at the available cores.

- Rust
Published by github-actions[bot] 10 months ago

irma-core - v0.4.1

Release Notes for v0.4.1 - 2025-04-28

Added

• The trimmer process now supports compressed fastq.gz files for both input and output.
• Adds flate2 crate as a dependency for handling .gz files

Changed

• The release process has been improved to produce better and more artifacts.

- Rust
Published by github-actions[bot] 10 months ago

irma-core - v0.0.0

Release Notes for v0.4.0 - 2025-04-16

Added

• trimmer now supports -f, --filter-widows for filtering widowed/orphaned reads in a paired-end context, with support for two input and two output fastq files.
• Github actions added to generate downloadable releases

Changed

• Updates dependencies, particularly with foldhash and zoe improvements
• For trimmer, long argument --fastq-output-file is now --fastq-output

Fixes

• For num-procs, the environemntal var LOCAL_PROCS_OVERRIDE now caps at the max available cores, consistent with the warning message.

- Rust
Published by github-actions[bot] 10 months ago

irma-core - v0.4.0

Release Notes for v0.4.0 - 2025-04-16

Added

• trimmer now supports -f, --filter-widows for filtering widowed/orphaned reads in a paired-end context, with support for two input and two output fastq files.
• Github actions added to generate downloadable releases

Changed

• Updates dependencies, particularly with foldhash and zoe improvements
• For trimmer, long argument --fastq-output-file is now --fastq-output

Fixes

• For num-procs, the environemntal var LOCAL_PROCS_OVERRIDE now caps at the max available cores, consistent with the warning message.

- Rust
Published by github-actions[bot] 11 months ago

irma-core - v0.0.0

- Rust
Published by github-actions[bot] 11 months ago