Nextflow Modules
Showing module(s) with keyword "convert"
| Module | Kind | Keywords | Description |
|---|---|---|---|
| nf-core/bamtofastq10x | Process | bam convert fastq 10x | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis |
| nf-core/bamtools/convert | Process | bamtools bamtools/convert bam convert bed fasta fastq json pileup sam yaml | BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. |
| nf-core/bcftools/convert | Process | bcftools convert vcf gvcf | Converts certain output formats to VCF |
| nf-core/bedops/convert2bed | Process | convert bed genomics | Convert BAM/GFF/GTF/GVF/PSL files to bed |
| nf-core/bio2zarr/vcf2zarrconvert | Process | vcf zarr convert genomics | Convert VCF data to the VCF Zarr specification reliably, in parallel or distributed over a cluster. |
| nf-core/bio2zarr/vcf2zarrexplode | Process | vcf icf zarr convert genomics | Convert VCF(s) to intermediate columnar format (ICF) |
| nf-core/custom/tabulartogseachip | Process | gsea chip convert tabular | Make a GSEA class file (.chip) from tabular inputs |
| nf-core/custom/tabulartogseacls | Process | gsea cls convert tabular | Make a GSEA class file (.cls) from tabular inputs |
| nf-core/eido/convert | Process | eido convert PEP format samplesheet | Convert any PEP project or Nextflow samplesheet to any format |
| nf-core/emboss/seqret | Process | emboss gff embl genbank fasta convert swissprot | Reads in one or more sequences, converts, filters, or transforms them and writes them out again |
| nf-core/fgumi/fastq | Process | bam fastq convert UMIs | Convert a BAM file to interleaved FASTQ format with fgumi |
| nf-core/gatk4/fastqtosam | Process | bam convert fastq gatk4 | Converts FastQ file to SAM/BAM format |
| nf-core/last/mafconvert | Process | LAST convert alignment MAF | Converts MAF alignments in another format. |
| nf-core/pbtk/bam2fastq | Process | convert bam genomics pacbio | converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq |
| nf-core/picard/bedtointervallist | Process | bed interval list picard convert | Creates an interval list from a bed file and a reference dict |
| nf-core/rastair/methylkit | Process | methylation rastair C->T conversion bisulphite bisulfite mCtoT methylkit convert parser | Parses rastair call output and converts it into a MethylKit-compatible format. |
| nf-core/sentieon/readwriter | Process | merge convert readwriter sentieon | Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file. |
| nf-core/seqkit/fq2fa | Process | fastq |