Trim sequencing adapters and collapse overlapping reads
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
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.
Output
name:type
description
pattern
singles_truncated
meta: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
${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
discarded
meta:file
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
*.discarded.fastq.gz
${prefix}.discarded.fastq.gz:file
Adapter trimmed FastQ files of reads that did not pass filtering
thresholds.
*.discarded.fastq.gz
paired_truncated
meta: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
${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
collapsed
meta:file
Collapsed FastQ of paired-end reads that successfully merged with their
respective R1 pair but were not trimmed.
*.collapsed.fastq.gz
${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
collapsed_truncated
meta: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
${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
paired_interleaved
meta:file
Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads
*.paired.fastq.gz
${prefix}.paired.fastq.gz:file
Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads
*.paired.fastq.gz
settings
meta:file
AdapterRemoval log file
*.settings
*.settings:file
AdapterRemoval log file
*.settings
versions
versions.yml:file
File containing software versions
versions.yml
Tools
adapterremoval
GPL v3
The AdapterRemoval v2 tool for merging and clipping reads.
