1.1.0

1.1.0

Quality of life update with a completely reworked report, new options to provide input data and some more experimental options for primer trimming and read merging. Details below:

Features

• New argument --reads is mutually exclusive with --input and takes a glob path as argument. File names are parsed with the glob pattern and paired. This allows bypassing the need for a sample-sheet. It is not recommended way to provide input data but can be helpful in many cases.

  nextflow run bio-raum/FooDMe2 -profile singularity --reads '/path/to/reads/*_R{1,2}_001.fastq.gz'
  

• Add the parameter --non_overlapping to simply concatenate R1 and R2 reads instead of merging with an overlapping sequence. This is useful in case the amplicon or seuqnce length produce reads with no overlaps.

• Add the argument --cutadapt_trim_flex to attempt trimming on both 5' and 3' of reads but also keep reads where only a 5' trimming was performed.

Reporting

• Complete rework of the HTML report: now uses a fully customized markdown template.
• Disabled hard filtering of samples based on read number after the primer trimming step. Samples will now soft fail in subsequent steps (e.g. clustering) or keep going to the end.
• All samples (including) failed samples now appear in the end report. Samples where no primmer trimming or clustering could be performed are marked as fail.
• Added read counts to the excel report

Documentation

• Added ressource usage arguments to usage documentation
• Added some information on the --reference_base argument in the troobleshooting section
• Added information on the new --reads argument
• Added information on the use of a local configuration file
• Added information on BLAST, and clustering-specific arguments

Bugs

• Fix conda environment definition path for module DADA2:RMCHIMERA that could lead to a failure to genreate the environment for conda user depending on the channel settings.
• Actually implements chimera removal skipping behaviour for --remove_chimera false
• Enforce similar filtering procedure for both VSEARCH and DADA2 workflows:
  • Filtering of sequences based on expected amplicon size (amplicon_min_size and amplicon_max_size) now correctly happens after read merging instead on being applied to the read length.
  • Filtering based on maxEE and maxNs now happens at the read level, prior to merging for VSEARCH
  • For both Workflows, read pairs are filtered baed on MaxEE and MaxNs, then merged, then merged pairs are filtered for expected size