bam_dedup_umi

BAM deduplication with UMI processing for both genome and transcriptome alignments

deduplicationUMIBAMgenometranscriptomeumicollapseumitools

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_dedup_umi

Description

BAM deduplication with UMI processing for both genome and transcriptome alignments

Input

name:type

description

pattern

`ch_genome_bam`

Channel with genome BAM files

`ch_fasta`

Channel with genome FASTA file

`umi_dedup_tool`

UMI deduplication tool to use

`umitools_dedup_stats`

Whether to generate UMI-tools deduplication stats

`bam_csi_index`

Whether to generate CSI index

`ch_transcriptome_bam`

Channel with transcriptome BAM files

`ch_transcript_fasta`

Channel with transcript FASTA file

Output

name:type

description

pattern

`bam`

Channel containing deduplicated genome BAM files

`bai`

Channel containing indexed BAM (BAI) files

`csi`

Channel containing CSI files (if bam_csi_index is true)

`dedup_log`

Channel containing deduplication log files

`stats`

Channel containing BAM statistics files

`flagstat`

Channel containing flagstat files

`idxstats`

Channel containing idxstats files

`multiqc_files`

Channel containing files for MultiQC

`transcriptome_bam`

Channel containing deduplicated transcriptome BAM files

`versions`

Channel containing software versions file