Workflow: bwa-mem-sort-distr.cwl

Fetched 2024-05-29 19:03:56 GMT
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Inputs

ID Type Title Doc
sample String (Optional)
library String (Optional)
threads Integer (Optional)
platform String (Optional)
readgroup String (Optional)
reference File
chunk_size Integer (Optional)
input_reads File[]
output_file String
sort_threads Integer (Optional)
extract_chunks String[]
mark_secondary Boolean (Optional)
sort_reference File (Optional)
bam_compression Integer (Optional)
min_std_max_min Integer[] (Optional)
advanced_options String[] (Optional)
minimum_seed_length Integer (Optional)
input_reads_index_file File

Steps

ID Runs Label Doc
bwa
../algo/bwa-mem-sort-with-fastq-slicer.cwl (CommandLineTool)
merge
../algo/bam-merge.cwl (CommandLineTool)

merge sorted bam files. If input bam files are in the order of coordinate, and no overlap, mergemode 10 can be used

Outputs

ID Type Label Doc
output File
Permalink: https://w3id.org/cwl/view/git/d20382adfe7285cb517a25d95d2bcb7586546e23/stage/bwa-mem-sort-distr.cwl