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biobox/CHANGELOG.md
CI 7645430e58 Build branch v0.1 with version v0.1.0 (b84b297) 
Build pipeline: viash-hub.biobox.v0.1-8mh8l

Source commit: b84b29747d

Source message: Bump version to v0.1.0
2024-06-24 09:29:14 +00:00

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biobox unreleased

BREAKING CHANGES

  • Change default multiple_sep to ; (PR #25). This aligns with an upcoming breaking change in Viash 0.9.0 in order to avoid issues with the current default separator : unintentionally splitting up certain file paths.

NEW FEATURES

  • arriba: Detect gene fusions from RNA-seq data (PR #1).

  • fastp: An ultra-fast all-in-one FASTQ preprocessor (PR #3).

  • busco:

    • busco/busco_run: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
    • busco/busco_list_datasets: Lists available busco datasets (PR #18).
    • busco/busco_download_datasets: Download busco datasets (PR #19).

  • cutadapt: Remove adapter sequences from high-throughput sequencing reads (PR #7).

  • featurecounts: Assign sequence reads to genomic features (PR #11).

  • bgzip: Add bgzip functionality to compress and decompress files (PR #13).

  • pear: Paired-end read merger (PR #10).

  • lofreq/call: Call variants from a BAM file (PR #17).

  • lofreq/indelqual: Insert indel qualities into BAM file (PR #17).

  • multiqc: Aggregate results from bioinformatics analyses across many samples into a single report (PR #42).

  • star:

    • star/star_align_reads: Align reads to a reference genome (PR #22).
    • star/star_genome_generate: Generate a genome index for STAR alignment (PR #58).

  • gffread: Validate, filter, convert and perform other operations on GFF files (PR #29).

  • salmon:

    • salmon/salmon_index: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
    • salmon/salmon_quant: Transcript quantification from RNA-seq data (PR #24).

  • samtools:

    • samtools/samtools_flagstat: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
    • samtools/samtools_idxstats: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
    • samtools/samtools_index: Index SAM/BAM/CRAM files (PR #35).
    • samtools/samtools_sort: Sort SAM/BAM/CRAM files (PR #36).
    • samtools/samtools_stats: Reports alignment summary statistics for a BAM file (PR #39).
    • samtools/samtools_faidx: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
    • samtools/samtools_collate: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
    • samtools/samtools_view: Views and converts SAM/BAM/CRAM files (PR #48).
    • samtools/samtools_fastq: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).

  • falco: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).

  • bedtools:

    • bedtools_getfasta: extract sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file (PR #59).

MINOR CHANGES

  • Uniformize component metadata (PR #23).

  • Update to Viash 0.8.5 (PR #25).

  • Update to Viash 0.9.0-RC3 (PR #51).

  • Update to Viash 0.9.0-RC6 (PR #63).

  • Switch to viash-hub/toolbox actions (PR #64).

DOCUMENTATION

  • Update README (PR #64).

BUG FIXES

  • Add escaping character before leading hashtag in the description field of the config file (PR #50).

  • Format URL in biobase/bcl_convert description (PR #55).

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