BAM deduplication with UMI processing for both genome and transcriptome alignments
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
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
