Workflow: sequence (bam or fastqs) to trimmed fastqs

Fetched 2024-06-20 07:03:39 GMT
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Workflow as SVG
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Inputs

ID Type Title Doc
adapters File
unaligned https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/types/sequence_data.yml#sequence_data
max_uncalled Integer
unzip_fastqs Boolean (Optional)
min_readlength Integer
adapter_trim_end String
adapter_min_overlap Integer

Steps

ID Runs Label Doc
trim_fastq
../tools/trim_fastq.cwl (CommandLineTool)
Trim FASTQ (flexbar)
sequence_to_fastq
../tools/sequence_to_fastq.cwl (CommandLineTool)
Picard: BAM to FASTQ

Outputs

ID Type Label Doc
fastq1 File
fastq2 File
fastqs File[]
Permalink: https://w3id.org/cwl/view/git/8da2b1cd6fa379b2c22baf9dad762d39630e6f46/definitions/subworkflows/sequence_to_trimmed_fastq.cwl