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

description

pattern

`ch_genome_bam`

Channel with genome BAM files

`ch_fasta_fai`

Channel with genome FASTA file and index

`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_fai`

Channel with transcript FASTA file and index

`umitools_dedup_primary_only`

Whether to filter to primary alignments before UMI-tools dedup

Output

name

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

`genome_stats`

Channel containing BAM statistics for the genome-aligned BAM only (transcriptome excluded)

`genome_flagstat`

Channel containing flagstat for the genome-aligned BAM only

`genome_idxstats`

Channel containing idxstats for the genome-aligned BAM only

`per_sample_mqc_bundle`

Per-sample MultiQC-feeding outputs (genome-side only: genomic dedup log,
genome stats, flagstat, idxstats) joined on meta. Transcriptome stats
excluded (MultiQC can’t disambiguate them from genome stats).

`multiqc_files`

Channel containing files for MultiQC

`transcriptome_bam`

Channel containing deduplicated transcriptome BAM files

`versions`

Channel containing software versions file