v1.3

• Debug fastq input_folder mode
• Simplify conda environment to speed up creation (use strict channel dependency, remove channel and some dependencies); this solves circleci timeout

v1.2

New feature:

• uses bwa-mem2 by default (closes issue #30 )
• docker and singularity images now contain bwa-mem2, but NOT conda env, because no receipe is available yet
• parameter bwa_mem allows to control the bwa call (use "bwa mem" to switch back to regular bwa)

v1.1

Novelties:

• allow arbitrarily many fastq files per sample in input_file mode
• add singularity file (closes issue #20 )
• change docker base image to something more stable, and rely on conda for installations (closes issue #19 )
• add parameters for providing multiqc config file and specifying AdapterRemoval options
• migrate to circleci2
• add bwa_option_M flag to trigger bwa option -M and the corresponding option in samblaster; default is now to NOT use this option

Other improvements:

• update conda env, add adapterremoval dependency (closes issue #19 )
• correct/update help

Version 1.0

First release of the pipeline