Description

Merge sorted fixmated BAM files with reference to an assembly, then optionally mark duplicates

Input

Name
Description
Pattern

ch_bam (file)

The input channel containing the BAM/CRAM/SAM files Structure: [ val(meta), path(bam) ]

*.{bam,cram,sam}

ch_assemblies (file)

Assemblies for merging and marking duplicates. Structure: [ val(meta), path(fasta) ]

*.{fasta,fasta.gz}

val_mark_duplicates (boolean)

Flag to trigger marking duplicates on the merged BAM files

Output

Name
Description
Pattern

bam (file)

Channel containing merged and possibly duplicate-marked BAM files Structure: [ val(meta), path(bam) ]

*.bam

bam_index (file)

Channel containing the index file(s) for the merged BAM Structure: [ val(meta), path(index) ]

*.{bai,csi,crai}

metrics (file)

Channel containing markdup metrics, if duplicates marked Structure: [ val(meta), path(index) ]

*.{bai,csi,crai}

Components

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