The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
- Fixed incorrect assignment of cluster groups (Issue #131).
- Improved TPM file splitting performance (Issue #120).
- Fixed an issue where R scripts altered sample names upon loading (Issue #122).
Patch for run_stager.R (#108) and template update v2.11.1 (#109).
Patch for run_drimseq_filter.R to cast command line arguments to numeric. See issue #98 on nf-core/rnasplice.
First release of nf-core/rnasplice, created with the nf-core template.
Implemented pipeline:
- Merge re-sequenced FastQ files (cat)
- Read QC (FastQC)
- Adapter and quality trimming (TrimGalore)
- Alignment with STAR:
- STAR -> Salmon
- STAR -> featureCounts
- STAR -> HTSeq (DEXSeq count)
- Sort and index alignments (SAMtools)
- Create bigWig coverage files (BEDTools, bedGraphToBigWig)
- Pseudo-alignment and quantification (Salmon; optional)
- Summarize QC (MultiQC)
- Differential Exon Usage (DEU):
- HTSeq -> DEXSeq
- featureCounts -> edgeR
- Quantification with featureCounts or HTSeq
- Differential exon usage with DEXSeq or edgeR
- Differential Transcript Usage (DTU):
- Salmon -> DRIMSeq -> DEXSeq
- Filtering with DRIMSeq
- Differential transcript usage with DEXSeq
- Event-based splicing analysis:
- STAR -> rMATS
- Salmon -> SUPPA2
Updated pipeline:
- Visualization of differential results with edgeR, DEXSeq, and MISO
- Contrasts specified using contrastsheet.csv
- Allow users to specify input data type and start point (e.g., fastq, genome_bam, transcript_bam, salmon_results)
- Pipeline schematic updated