nf-core/abyss/abysspe @ 0.0.0-0c7146d
ABySS is a de novo sequence assembler intended for short paired-end reads and genomes of all sizes.
| Tool | Description | Homepage |
|---|---|---|
| abyss | Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler. | https://github.com/bcgsc/abyss/blob/v2.3.10/README.md |
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` |
|---|---|
reads
file
|
List of input paired-end FastQ files (R1 and R2).
Must be paired-end reads; ABySS requires paired reads for assembly.
*.{fastq.gz,fastq,fq.gz,fq}
|
merged
file
|
Optional merged/overlapping paired-end reads or supplementary single-end reads.
Use empty list `[]` if not available.
*.{fastq.gz,fastq,fq.gz,fq}
|
kmersize
integer
|
K-mer size for assembly. Must be an odd number. |
|---|
Output
5 channels
#1
log
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1' ]` |
|---|---|
*-abyss.log
file
|
ABySS assembly log file
*-abyss.log
|
#2
stats
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1' ]` |
|---|---|
*-stats
file
|
Assembly statistics file
*-stats
|
#3
contigs
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1' ]` |
|---|---|
*-contigs.fa.gz
file
|
Assembled contigs in FASTA format
*-contigs.fa.gz
|
#4
scaffolds
tuple
meta
map
|
Groovy Map containing sample information e.g. `[ id:'sample1' ]` |
|---|---|
*-scaffolds.fa.gz
file
|
Assembled scaffolds in FASTA format
*-scaffolds.fa.gz
|
#5
versions_abyss
tuple
${task.process}
string
|
The name of the process |
|---|---|
abyss
string
|
The name of the tool |
abyss-pe version | grep abyss | cut -d" " -f3
eval
|
The expression to obtain the version of the tool |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 0c7146d85582628b5d1034504702fa808632b1af |
| Release Date | 08 Apr 2026 18:41:20 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fabyss%2Fabysspe/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/abyss/abysspe/blobs/sha256:108ed6f9ad0c201cc604cd40f729d522e7b6614b9f56fc9bf6c9d2adc3742a40 |
| Size | 3.2 KB |
| Checksum | sha256:108ed6f9ad0c201cc604cd40f729d522e7b6614b9f56fc9bf6c9d2adc3742a40 |
| Downloads | 5 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:41:20 (UTC) | PUBLISHED | 5 | 3.2 KB |