81 lines
3.2 KiB
Markdown
81 lines
3.2 KiB
Markdown
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# biobox unreleased
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## BREAKING CHANGES
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* Change default `multiple_sep` to `;` (PR #25). This aligns with an upcoming breaking change in
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Viash 0.9.0 in order to avoid issues with the current default separator `:` unintentionally
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splitting up certain file paths.
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## NEW FEATURES
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* `arriba`: Detect gene fusions from RNA-seq data (PR #1).
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* `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3).
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* `busco`:
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- `busco/busco_run`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6).
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- `busco/busco_list_datasets`: Lists available busco datasets (PR #18).
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- `busco/busco_download_datasets`: Download busco datasets (PR #19).
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* `cutadapt`: Remove adapter sequences from high-throughput sequencing reads (PR #7).
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* `featurecounts`: Assign sequence reads to genomic features (PR #11).
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* `bgzip`: Add bgzip functionality to compress and decompress files (PR #13).
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* `pear`: Paired-end read merger (PR #10).
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* `lofreq/call`: Call variants from a BAM file (PR #17).
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* `lofreq/indelqual`: Insert indel qualities into BAM file (PR #17).
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* `multiqc`: Aggregate results from bioinformatics analyses across many samples into a single report (PR #42).
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* `star`:
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- `star/star_align_reads`: Align reads to a reference genome (PR #22).
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- `star/star_genome_generate`: Generate a genome index for STAR alignment (PR #58).
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* `gffread`: Validate, filter, convert and perform other operations on GFF files (PR #29).
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* `salmon`:
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- `salmon/salmon_index`: Create a salmon index for the transcriptome to use Salmon in the mapping-based mode (PR #24).
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- `salmon/salmon_quant`: Transcript quantification from RNA-seq data (PR #24).
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* `samtools`:
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- `samtools/samtools_flagstat`: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).
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- `samtools/samtools_idxstats`: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
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- `samtools/samtools_index`: Index SAM/BAM/CRAM files (PR #35).
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- `samtools/samtools_sort`: Sort SAM/BAM/CRAM files (PR #36).
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- `samtools/samtools_stats`: Reports alignment summary statistics for a BAM file (PR #39).
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- `samtools/samtools_faidx`: Indexes FASTA files to enable random access to fasta and fastq files (PR #41).
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- `samtools/samtools_collate`: Shuffles and groups reads in SAM/BAM/CRAM files together by their names (PR #42).
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- `samtools/samtools_view`: Views and converts SAM/BAM/CRAM files (PR #48).
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- `samtools/samtools_fastq`: Converts a SAM/BAM/CRAM file to FASTQ (PR #52).
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* `falco`: A C++ drop-in replacement of FastQC to assess the quality of sequence read data (PR #43).
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* `bedtools`:
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- `bedtools_getfasta`: extract sequences from a FASTA file for each of the
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intervals defined in a BED/GFF/VCF file (PR #59).
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## MINOR CHANGES
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* Uniformize component metadata (PR #23).
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* Update to Viash 0.8.5 (PR #25).
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* Update to Viash 0.9.0-RC3 (PR #51).
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* Update to Viash 0.9.0-RC6 (PR #63).
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* Switch to viash-hub/toolbox actions (PR #64).
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## DOCUMENTATION
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* Update README (PR #64).
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## BUG FIXES
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* Add escaping character before leading hashtag in the description field of the config file (PR #50).
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* Format URL in biobase/bcl_convert description (PR #55).
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