v0.3.0

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).

• cellranger:

  • cellranger/cellranger_mkref: Build a Cell Ranger-compatible reference folder from user-supplied genome FASTA and gene GTF files (PR #164).

• 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).

• sgedemux: demultiplexing sequencing data generated on Singular Genomics' sequencing instruments (PR #166).

• bases2fasta: demultiplexing sequencing data generated by Element Biosciences instruments (PR #167).

BUG FIXES

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

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

• bbmap_bbsplit: Change argument type of build to file and add output argument index (PR #162).

• kallisto/kallisto_index: Fix command script to use --threads option (PR #162).

• kallisto/kallisto_quant: Change type of argument output_dir to file and add output argument log (PR #162).

• rsem/rsem_calculate_expression: Fix output handling (PR #162).

• sortmerna: Change type pf argument aligned to file; update docker image; accept more than two reference files (PR #162).

• umi_tools/umi_tools_extract: Remove umi_discard_reads option and change log2stderr to input argument (PR #162).

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.

• bbmap_bbsplit: Move to namespace bbmap (PR #162).