Workflow: umi molecular alignment fastq workflow

Fetched 2023-01-04 10:07:22 GMT
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Inputs

ID Type Title Doc
platform String[]
reference File
read1_fastq File[]
read2_fastq File[]
sample_name String
library_name String[]
platform_unit String[]
read_structure String[]
target_intervals File (Optional)

Steps

ID Runs Label Doc
index_cram
../tools/index_cram.cwl (CommandLineTool)
samtools index cram
bam_to_cram
../tools/bam_to_cram.cwl (CommandLineTool)
BAM to CRAM conversion
fastq_to_bam
../tools/fastq_to_bam.cwl (CommandLineTool)
fastq to bam
alignment_workflow umi molecular alignment workflow

Outputs

ID Type Label Doc
aligned_cram File
adapter_histogram File[]
duplex_seq_metrics File[]
Permalink: https://w3id.org/cwl/view/git/e8b7759826df40b8bb821b40b15aea960a4951c4/definitions/pipelines/alignment_umi_molecular.cwl