CHANGELOG.md

biobox x.x.x

NEW FUNCTIONALITY

• agat:

  • agat/agat_convert_genscan2gff: convert a genscan file into a GFF file (PR #100).
  • agat/agat_sp_add_introns: add intron features to gtf/gff file without intron features (PR #104).
  • agat/agat_sp_filter_feature_from_kill_list: remove features in a GFF file based on a kill list (PR #105).
  • agat/agat_sp_merge_annotations: merge different gff annotation files in one (PR #106).
  • agat/agat_sp_statistics: provides exhaustive statistics of a gft/gff file (PR #107).
  • agat/agat_sq_stat_basic: provide basic statistics of a gtf/gff file (PR #110).

• bd_rhapsody/bd_rhapsody_sequence_analysis: BD Rhapsody Sequence Analysis CWL pipeline (PR #96).

• bedtools:

  • bedtools/bedtools_bamtobed: Converts BAM alignments to BED6 or BEDPE format (PR #109).

• rsem/rsem_calculate_expression: Calculate expression levels (PR #93).

• rseqc:

  • rseqc/rseqc_inner_distance: Calculate inner distance between read pairs (PR #159).
  • rseqc/rseqc_inferexperiment: Infer strandedness from sequencing reads (PR #158).
  • rseqc/bam_stat: Generate statistics from a bam file (PR #155).

• nanoplot: Plotting tool for long read sequencing data and alignments (PR #95).

BUG FIXES

• falco: Fix a typo in the --reverse_complement argument (PR #157).

• cutadapt: Fix the the non-functional action parameter (PR #161).

MINOR CHANGES

• agat_convert_bed2gff: change type of argument inflate_off from boolean_false to boolean_true (PR #160).

• cutadapt: change type of argument no_indels and no_match_adapter_wildcards from boolean_false to boolean_true (PR #160).

• Upgrade to Viash 0.9.0.

biobox 0.2.0

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).
  • agat_convert_bed2gff: convert bed file to gff format (PR #97).
  • agat_convert_embl2gff: convert an EMBL file into GFF format (PR #99).
  • agat/agat_convert_sp_gff2gtf: convert any GTF/GFF file into a proper GTF file (PR #76).
  • agat/agat_convert_bed2gff: convert bed file to gff format (PR #97).
  • agat/agat_convert_mfannot2gff: convert MFannot "masterfile" annotation to gff format (PR #112).
  • agat/agat_convert_embl2gff: convert an EMBL file into GFF format (PR #99).
  • agat/agat_convert_sp_gff2tsv: convert gtf/gff file into tabulated file (PR #102).
  • agat/agat_convert_sp_gxf2gxf: fixes and/or standardizes any GTF/GFF file into full sorted GTF/GFF file (PR #103).

• bedtools:

  • bedtools/bedtools_intersect: Allows one to screen for overlaps between two sets of genomic features (PR #94).
  • bedtools/bedtools_sort: Sorts a feature file (bed/gff/vcf) by chromosome and other criteria (PR #98).
  • bedtools/bedtools_genomecov: Compute the coverage of a feature file (bed/gff/vcf/bam) among a genome (PR #128).
  • bedtools/bedtools_groupby: Summarizes a dataset column based upon common column groupings. Akin to the SQL "group by" command (PR #123).
  • bedtools/bedtools_merge: Merges overlapping BED/GFF/VCF entries into a single interval (PR #118).
  • bedtools/bedtools_bamtofastq: Convert BAM alignments to FASTQ files (PR #101).
  • bedtools/bedtools_bedtobam: Converts genomic feature records (bed/gff/vcf) to BAM format (PR #111).
  • bedtools/bedtools_bed12tobed6: Converts BED12 files to BED6 files (PR #140).
  • bedtools/bedtools_links: Creates an HTML file with links to an instance of the UCSC Genome Browser for all features / intervals in a (bed/gff/vcf) file (PR #137).

• qualimap/qualimap_rnaseq: RNA-seq QC analysis using qualimap (PR #74).

• rsem/rsem_prepare_reference: Prepare transcript references for RSEM (PR #89).

• bcftools:

  • bcftools/bcftools_concat: Concatenate or combine VCF/BCF files (PR #145).
  • bcftools/bcftools_norm: Left-align and normalize indels, check if REF alleles match the reference, split multiallelic sites into multiple rows; recover multiallelics from multiple rows (PR #144).
  • bcftools/bcftools_annotate: Add or remove annotations from a VCF/BCF file (PR #143).
  • bcftools/bcftools_stats: Parses VCF or BCF and produces a txt stats file which can be plotted using plot-vcfstats (PR #142).
  • bcftools/bcftools_sort: Sorts BCF/VCF files by position and other criteria (PR #141).

• fastqc: High throughput sequence quality control analysis tool (PR #92).

• sortmerna: Local sequence alignment tool for mapping, clustering, and filtering rRNA from metatranscriptomic data (PR #146).

• fq_subsample: Sample a subset of records from single or paired FASTQ files (PR #147).

• kallisto:

  • kallisto_index: Create a kallisto index (PR #149).
  • kallisto_quant: Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads (PR #152).

• trimgalore: Quality and adapter trimming for fastq files (PR #117).

MINOR CHANGES

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

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

• Update several components in order to avoid duplicate code when using unset on boolean arguments (PR #133).

• Bump viash to 0.9.0-RC7 (PR #134)

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).
  • umi_tools/umi_tools_prepareforrsem: Fix paired-end reads in name sorted BAM file to prepare for RSEM (PR #148).

• 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).

• bbmap:

  • bbmap_bbsplit: Split sequencing reads by mapping them to multiple references simultaneously (PR #138).

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).