htrnaseq/CHANGELOG.md

htrnaseq v0.x.x

New functionality

• Added umi_length argument (PR #27).
• Added runner workflow (PR #26, see below)

runner workflow

• Removed wellBarcodesLength from parallel_map workflow (PR #27).

Major changes

A runner workflows has been added, providing two additional features:

1. Start from an input directory containing fastq files rather than a list of input fastq pairs.
2. Improve the output of the workflow

Input directory

It is now possible to specify a single --input <basedir> directory as input and the runner will extract the fastq file pairs. An error will be raised if the filename processing leads to errors.

Output

The runner provides a complete different approach to output. A couple of things are important here:

• Output is split up in 2 parts:

  1. The well-demultiplexed fastq files (--fastq_publish_dir)
  2. All the other results of the workflow (--results_publish_dir)

• The well-demultiplexed fastq file are stored under --fastq_publish_dir according to the following format:

  $fastq_publish_dir/$id/<date-time>_htrnaseq_<version>/$plate_$lane/<well_id>_R1/2_001.fastq
  

• The other results are stored under --results_publish_dir according to the following format:

  $results_publish_dir/$project_id/$experiment_id/<date-time>_htrnaseq_<version>/
  

  This is an example listing of this directory:

  esets
  fData
  nrReadsNrGenesPerChrom
  pData
  report.html
  star_output
  starLogs
  

This output structure can be circumvented by using the --output_dir option, which will store all output in a single directory.

1. Using the htrnaseq workflow directory rather than the runner interface
2. Using the argument --plain_output with the runner. fastq files and other results will still be published in their respective directories, but not in a directory hierarchy as described above.

Minor changes

• Use v0.2.0 version of cutadapt instead of main (PR #23).
• Use v0.3.0 version of cutadapt
• Bump viash to 0.9.1 (PR #31).
• create_eset: Update base container image, R version and all dependencies to newer versions (PR #28).

htrnaseq v0.2.0

New functionality

• Make sure that the Well ID matches the required format (PR #22 and PR #21).

htrnaseq v0.1.0

Initial release