meta map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
reads file	List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. *.{fq,fastq,fq.gz,fastq.gz}

adapterlist file	Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args.

meta map	Groovy Map containing sample information
*.settings file	AdapterRemoval log file *.settings

meta map	Groovy Map containing sample information
${prefix}.collapsed.fastq.gz file	Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair but were not trimmed. *.collapsed.fastq.gz

meta map	Groovy Map containing sample information
${prefix}.discarded.fastq.gz file	Adapter trimmed FastQ files of reads that did not pass filtering thresholds. *.discarded.fastq.gz

meta map	Groovy Map containing sample information
${prefix}.pair{1,2}.truncated.fastq.gz file	Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge with their respective R{1,2} pair due to long templates. The respective pair is stored in 'pair{1,2}_truncated'. *.pair{1,2}.truncated.fastq.gz

meta map	Groovy Map containing sample information
${prefix}.truncated.fastq.gz file	Adapter trimmed FastQ files of either single-end reads, or singleton 'orphaned' reads from merging of paired-end data (i.e., one of the pair was lost due to filtering thresholds). *.truncated.fastq.gz

meta map	Groovy Map containing sample information
${prefix}.paired.fastq.gz file	Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads *.paired.fastq.gz

meta map	Groovy Map containing sample information
${prefix}.collapsed.truncated.fastq.gz file	Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair and were trimmed of adapter due to sufficient overlap. *.collapsed.truncated.fastq.gz

${task.process} string	The name of the process
AdapterRemoval string	The name of the tool
AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" eval	The expression to obtain the version of the tool