Nextflow Modules
Showing module(s) with keyword "immcantation"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/presto/assemblepairs | Process | immcantation airrseq paired-end assembly immunoinformatics fastq | Assembles paired-end reads into single reads using pRESTO AssemblePairs.py. The `mode` input selects the subcommand: `align`, `join`, `reference` or `sequential`. The subcommands share the same inputs, outputs and options, so they are exposed through one module rather than four; only `reference` and `sequential` use the reference input. The `reference` and `sequential` modes default to `--aligner usearch`, which is not in the container; pass `--aligner blastn` through `ext.args`. The module sets `--nproc ${task.cpus}`; with more than one process the order of the output records is not deterministic. Output FASTQ file names follow the input extension (e.g. `.fastq` or `.fq.gz`). |
| nf-core/presto/filterseq | Process | immcantation airrseq genomics immunoinformatics | Filter reads by quality score. |
| nf-core/presto/pairseq | Process | immcantation airrseq genomics immunoinformatics | Sorts and matches sequence records with matching coordinates across files |