Nextflow Modules
Showing module(s) with keyword "extract"
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/spextractsequences | genomics gff extract fasta sequence feature | This script extracts sequences in fasta format according to features described in a gff file. |
| nf-core/fgumi/extract | umi extract fastq bam | Extract unique molecular indices (UMIs) from FASTQ files and write an unaligned BAM file. |
| nf-core/modkit/extractcalls | modkit methylation extract calls read-level modbam nanopore ont | Produce a per-read per-position table of base modification **calls** (pass/fail/filtered, with the called base) from a modBAM using the same thresholding algorithm as `modkit pileup`. Complementary to `modkit extract full`, which emits raw probabilities: `extract calls` emits the thresholded categorical decision per site per read. |
| nf-core/modkit/extractfull | modkit methylation extract read-level modbam nanopore ont | Transform the probabilities from the MM/ML tags in a modBAM into a tab-separated per-read-per-position table. Emits one row for every modified-base probability call in every read — useful for downstream custom filtering, plotting, and ML training. Optionally BGZF-compressed via `--bgzf` in `ext.args`. |
| nf-core/picard/extractfingerprint | picard extract fingerprint bam | Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites. |
| nf-core/plink2/extract | plink2 extract identifiers | Subset plink pfiles with a text file of variant identifiers |
| nf-core/plink/extract | extract plink subset bfiles | Subset plink bfiles with a text file of variant identifiers |
| nf-core/tabix/tabix | index tabix vcf extract regions | DEPRECATED. Use HTSLIB/BGZIPTABIX instead. Create a tabix index from a sorted bgzip TAB-delimited genome file, or extract regions from a bgzipped VCF file using an optional regions file. |
| nf-core/umitools/extract | UMI barcode extract umitools | Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place |
| nf-core/untar | untar uncompress extract | Extract files from tar, tar.gz, tar.bz2, tar.xz archives |