biobox/CHANGELOG.md

biobox x.x.x

BREAKING CHANGES

• star/star_align_reads: Change all arguments from --camelCase to --snake_case (PR #62).

• star/star_genome_generate: Change all arguments from --camelCase to --snake_case (PR #62).

NEW FUNCTIONALITY

• star/star_align_reads: Add star solo related arguments (PR #62).

• bd_rhapsody/bd_rhapsody_make_reference: Create a reference for the BD Rhapsody pipeline (PR #75).

• umitools/umitools_dedup: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read (PR #54).

• seqtk:

  • seqtk/seqtk_sample: Subsamples sequences from FASTA/Q files (PR #68).
  • seqtk/seqtk_subseq: Extract the sequences (complete or subsequence) from the FASTA/FASTQ files based on a provided sequence IDs or region coordinates file (PR #85).

• agat/agat_convert_sp_gff2gtf: convert any GTF/GFF file into a proper GTF file (PR #76).

MINOR CHANGES

• busco components: update BUSCO to 5.7.1 (PR #72).

• Update CI to reusable workflow in viash-io/viash-actions (PR #86).

DOCUMENTATION

• Extend the contributing guidelines (PR #82):

  • Update format to Viash 0.9.

  • Descriptions should be formatted in markdown.

  • Add defaults to descriptions, not as a default of the argument.

  • Explain parameter expansion.

  • Mention that the contents of the output of components in tests should be checked.

• Add authorship to existing components (PR #88).

BUG FIXES

• pear: fix component not exiting with the correct exitcode when PEAR fails (PR #70).

• cutadapt: fix --par_quality_cutoff_r2 argument (PR #69).

• cutadapt: demultiplexing is now disabled by default. It can be re-enabled by using demultiplex_mode (PR #69).

• multiqc: update multiple separator to ; (PR #81).

biobox 0.1.0

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).
  • samtools/samtools_fastq: Converts a SAM/BAM/CRAM file to FASTA (PR #53).

• umi_tools: -umi_tools/umi_tools_extract: Flexible removal of UMI sequences from fastq reads (PR #71).

• 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).