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Change log for dada2-nf

2.0.3

  • New filter_and_trim output dir with filtered and dropped fastqs (GH87)

2.0.2

  • Unmerged reads now included in output (GH84)

2.0.1

2.0.0

  • DSL 2 pipeline
  • In params.json sample_information and fastq_list must match or error
  • Switching to vsearch --iddef 0 clustering setting

1.19

  • Clustering fwd and rev reads by sampleid (GH65)
  • New counts file reports read counts at each step plus yield and denominator
  • All filtered fwd and rev oriented reads are included in output (including unmerged) in seqtab_f.csv and seqtab_R.csv
  • Filtered R1 and R2 reads are now included in output
  • All off_target reads included in output

1.18.1

  • Optionally include cutadapt to remove adapters (GH55)
  • Docker image is built on Ubuntu 22.04 base (GH56)
  • Docker image is hosted by GutHub container registry
  • Simplify Docker and Singularity configuration; there is no longer a Singularity image associated with this project (both Docker and Singularity use the same image hosted on ghcr).
  • Update GH action to build image and test sequentially; does not push latest tag to container registry except on tagged releases.
  • Sort unmerged read fasta files in order of descending abundance (GH59)

1.17.1

  • Support for ITS using vsearch alignments
  • Handle null seqtab in get_chim_dropped.R

1.16.1

  • Actually implements get_unmerged task
  • Add script get_dropped_chim.R identifying SV dropped as chimeras

1.15.2

  • Implement downsampling (GH44)
  • get_unmerged task saves empty file when there are no merged reads

1.15.1

  • bugfix: fix column names in ljoin.R (GH40)

1.15

  • New downsample: [int] argument in params (GH38)
  • use dada2 1.18
  • output includes files containing unmerged reads (GH11)
  • remove native Singularity build file

1.14

  • Handle mixed reads in either direction (GH37)

1.13