- Change default
multiple_septo;(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.
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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).
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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). -
star/star_align_reads: Align reads to a reference genome (PR #22). -
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).
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samtools:samtools/flagstat: Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type (PR #31).samtools/idxstats: Reports alignment summary statistics for a SAM/BAM/CRAM file (PR #32).
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Uniformize component metadata (PR #23).
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Update to Viash 0.8.5 (PR #25).