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

`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

`index`

Channel containing the index of the deduplicated genome BAM

`genomic_dedup_log`

Channel containing deduplication log files for the genome BAM

`transcriptomic_dedup_log`

Channel containing deduplication log files for the transcriptome BAM

`prepare_for_rsem_log`

Channel containing the UMI-tools prepare_for_rsem log for paired-end BAM files

`stats`

Channel containing BAM statistics files for both genome and transcriptome BAMs

`flagstat`

Channel containing flagstat files for both genome and transcriptome BAMs

`idxstats`

Channel containing idxstats files for both genome and transcriptome BAMs

`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

`tsv_edit_distance`

Channel containing the UMI-tools edit distance TSV, reporting the
edit distance between the UMIs at each position. Only populated when
umi_dedup_tool is ‘umitools’.

`tsv_per_umi`

Channel containing the UMI-tools per UMI TSV, reporting UMI-level summary
statistics. Only populated when umi_dedup_tool is ‘umitools’.

`tsv_umi_per_position`

Channel containing the UMI-tools TSV tabulating the counts for unique
combinations of UMI and position. Only populated when umi_dedup_tool is
‘umitools’.

`multiqc_files`

Channel containing files for MultiQC

`transcriptome_bam`

Channel containing the final deduplicated transcriptome BAM files

`transcriptome_dedup_bam`

Channel containing the transcriptome BAM after deduplication, before name sorting

`transcriptome_sorted_bam`

Channel containing the name-sorted deduplicated transcriptome BAM

`transcriptome_sorted_bam_index`

Channel containing the index of the coordinate-sorted deduplicated transcriptome BAM

`transcriptome_filtered_bam`

Channel containing the paired-end transcriptome BAM filtered by UMI-tools prepare_for_rsem

`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).