Nextflow Modules
Showing module(s) with keyword "conversion"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| cellgeni/sra2fastq | Process | SRA FASTQ conversion single-cell 10x public data | Converts a local SRA file to split gzipped FASTQ files using parallel-fastq-dump, producing one FASTQ per read slot ready for downstream processing. |
| nf-core/agat/convertbed2gff | Process | genome bed gff conversion | Takes a bed12 file and converts to a GFF3 file |
| nf-core/agat/convertgff2bed | Process | genome bed gff conversion | Takes a GFF3 file and converts to a bed12 file |
| nf-core/agat/convertspgff2gtf | Process | genome gff gtf conversion | Converts a GFF/GTF file into a proper GTF file |
| nf-core/agat/convertspgff2tsv | Process | genome gff gtf conversion tsv | Converts a GFF/GTF file into a TSV file |
| nf-core/agat/convertspgxf2gxf | Process | genome gff gtf conversion | Fixes and standardizes GFF/GTF files and outputs a cleaned GFF/GTF file |
| nf-core/anndata/convert | Process | single-cell anndata conversion | Convert an AnnData H5AD file to Seurat and SingleCellExperiment RDS objects |
| nf-core/any2fasta | Process | fasta conversion sequences format genomics | Convert various sequence formats (GenBank, GFF, FASTQ, FASTA, CLUSTAL, Stockholm, GFA) to FASTA format. Input files may be gzip, bzip2, zip, or zstd compressed. |
| nf-core/bedgovcf | Process | bed vcf conversion variants | Convert a BED file to a VCF file according to a YAML config |
| nf-core/bedgraph_bedclip_bedgraphtobigwig | Workflow | bedgraph bigwig clip conversion | Convert bedgraph to bigwig with clip |
| nf-core/bedops/gtf2bed | Process | gtf bed conversion | Convert gtf format to bed format |
| nf-core/biomformat/convert | Process | biom feature table formatting conversion amplicon sequences metagenomics metatranscriptomics | Convert biom table to different format. Conversion between text tab-delimited, BIOM-v1 (JSON), and BIOM-v2 (HDF5) formats are supported |
| nf-core/duckdb/table2parquet | Process | parquet csv tsv conversion | Convert a delimited text table (CSV or TSV, gzipped or not) to Parquet. DuckDB types each column from the first 20480 rows and reads only the empty string as missing. Pass `read_csv` options through `ext.args`, for example `nullstr=['NA','']` for tables written by R. |
| nf-core/eautils/gtf2bed | Process | gtf gff bed bed12 annotation conversion | Convert a GTF/GFF annotation file to BED12 format |
| nf-core/gatk4/intervallisttobed | Process | bed conversion gatk4 interval | Converts an Picard IntervalList file to a BED file. |
| nf-core/gffread | Process | gff conversion validation | Validate, filter, convert and perform various other operations on GFF files |
| nf-core/gtdbtk/gtdbtoncbimajorityvote | Process | gtdb taxonomy ncbi taxonomy taxonomic classification conversion taxonomy classification genome taxonomy database bacteria archaea | Converts the output classifications of GTDB-TK from GTDB taxonomy to NCBI taxonomy |
| nf-core/manta/convertinversion | Process | structural variants conversion |