name: adapterremoval description: Trim sequencing adapters and collapse overlapping reads keywords: - trimming - adapters - merging - fastq tools: - adapterremoval: description: The AdapterRemoval v2 tool for merging and clipping reads. homepage: https://github.com/MikkelSchubert/adapterremoval documentation: https://adapterremoval.readthedocs.io licence: ["GPL v3"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - adapterlist: type: file description: 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. output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - singles_truncated: type: file description: | 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). pattern: "*.truncated.fastq.gz" - discarded: type: file description: | Adapter trimmed FastQ files of reads that did not pass filtering thresholds. pattern: "*.discarded.fastq.gz" - pair1_truncated: type: file description: | Adapter trimmed R1 FastQ files of paired-end reads that did not merge with their respective R2 pair due to long templates. The respective pair is stored in 'pair2_truncated'. pattern: "*.pair1.truncated.fastq.gz" - pair2_truncated: type: file description: | Adapter trimmed R2 FastQ files of paired-end reads that did not merge with their respective R1 pair due to long templates. The respective pair is stored in 'pair1_truncated'. pattern: "*.pair2.truncated.fastq.gz" - collapsed: type: file description: | Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair but were not trimmed. pattern: "*.collapsed.fastq.gz" - collapsed_truncated: type: file description: | Collapsed FastQ of paired-end reads that successfully merged with their respective R1 pair and were trimmed of adapter due to sufficient overlap. pattern: "*.collapsed.truncated.fastq.gz" - log: type: file description: AdapterRemoval log file pattern: "*.settings" - versions: type: file description: File containing software versions pattern: "versions.yml" authors: - "@maxibor" - "@jfy133"