Nextflow Registry | nf-core/elprep/filter@0.0.0-6c4ed3a

nf-core/elprep/filter @ 0.0.0-6c4ed3a

Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.

sort bam sam filter variant calling

Latest version: 0.0.0-6c4ed3a

Total downloads: 10

Source: nf-core/modules

Authors: @matthdsm

Maintainers: @matthdsm

Filter, sort and markdup sam/bam files, with optional BQSR and variant calling.

Add the following snippet to your workflow script to include this module.

include { ELPREP_FILTER } from 'nf-core/elprep/filter'

MIT License

Process

`Name`	`ELPREP_FILTER`

Input 9 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`bam` file	Input SAM/BAM file `*.{bam,sam}`
`bai` file	Input BAM file index `*.bai`
`target_regions_bed` file	Optional BED file containing target regions for BQSR and variant calling. `*.bed`
`filter_regions_bed` file	Optional BED file containing regions to filter. `*.bed`
`intermediate_bqsr_tables` file	Optional list of BQSR tables, used when parsing files created by `elprep split` `*.table`
`recall_file` file	Recall file with intermediate results for bqsr `*.recall`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reference_sequences` file	Optional SAM header to replace existing header. `*.sam`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`reference_elfasta` file	Elfasta file, required for BQSR and variant calling. `*.elfasta`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`known_sites_elsites` file	Optional elsites file containing known SNPs for BQSR. `*.elsites`

`run_haplotypecaller` boolean	Run variant calling on the input files. Needed to generate gvcf output.

`run_bqsr` boolean	Run BQSR on the input files. Needed to generate recall metrics.

`bqsr_tables_only` boolean	Write intermediate BQSR tables, used when parsing files created by `elprep split`.

`get_activity_profile` boolean	Get the activity profile calculated by the haplotypecaller to the given file in IGV format.

`get_assembly_regions` boolean	Get the assembly regions calculated by haplotypecaller to the specified file in IGV format.

Output 9 channels

#1 bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.{bam,sam}` file	BAM/SAM file `*.{bam,sam}`

#2 gvcf tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.vcf.gz` file	VCF file `*.{vcf.gz}`

#3 logs tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.log` file	Log file `elprep-*.log`

#4 table tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.table` file	Table `*.{table}`