0.26.0

• add parameters file for top-up merge
• functional equivalence: enable selection of markdup method - biobambam (default), samtools or picard

0.25.0

• add target autosome stats file generation to final_output_prep
• library merge:
  cram_write_option (default: use_tears, option use_local)
  updated templates to v2.0 format
• add options to standard stage2 templates to handle realignment

0.24.2

release 0.24.2

release 0.24.0

• allow format selection for stage1 outputs/stage2 inputs (default: cram)
• stage1 adapter detection now done in parallel with phix alignment
• add samtools stats qc check to stage1 analysis
• stage2 analysis templates amended to allow merging of multiple inputs; application of spatial_filter moved from stage1
• RNA alignments handle single-end runs
• new hisat2 alignment method
• use compressed fastq input for star alignment
• salmon quantification
  check that there are enough reads in the fastq file inputs
  check if quant file is present before copying it
  connect zip node to quant_genes node to ensure zip waits for salmon
• post_alignment_realignment.json: new port specification format

0.23.0

• target stats (samtools) addition to final output prep

0.22.1

• add default ("ifnull":"salmon") value for quant_method parameter to fix star/tophat2 tag#0 problem

0.22.0

• new template for minimap2 alignment, with optional post-alignment filtering of secondary and supplementary alignments, and minimap2_F_value parameter to allow non-default insert size to be specified (-F flag)
• subsampling of 10K reads (fastq produced by samtools view -s SEED.FRAC) and production of fastqcheck files added to stage1 and stage2 analyses (nchs, single-/paired-end)
• add lane-level samtools stats to stage1
• spatial filter application moved to stage2 from stage1
• amend spatial_filter input/output file names for easier identification
• empty edge entries recognised as noop - filter in viv.pl, ignore in visualisation, do not apply VTFILE
  prefixes when there are no to and from attributes

0.21.0

• salmon_alignment: copy quant.genes.sf to archive directory
• star_alignment: assign appropriate suffixes to bamtofastq output files
• merge: flag change for use with tears 1.2.4

0.20.1

• star_alignment
  correct version number (to 2.0)
  do queryname sort after alignment
• upgrade realignment template to version 2
• viv.pl: loosen overly strict checks when using output file nodes with subtype dummy

0.20.0

0.20.0