Workflow: bam to trimmed fastqs and HISAT alignments

Fetched 2020-07-14 15:58:36 GMT
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Inputs

ID Type Title Doc
firststrand Boolean (Optional)
adapters File
reference_index File
secondstrand Boolean (Optional)
min_readlength Integer
adapter_trim_end String
adapter_min_overlap Integer
max_uncalled Integer
read_group_fields String[]
read_group_id String
bam File

Steps

ID Runs Label Doc
trim_fastq
trim_fastq.cwl (CommandLineTool)
Trim FASTQ (flexbar)
bam_to_fastq
bam_to_fastq.cwl (CommandLineTool)
Picard: BAM to FASTQ
hisat2_align
hisat2_align.cwl (CommandLineTool)
HISAT2: align

Outputs

ID Type Label Doc
aligned_bam File
fastqs File[]
Permalink: https://w3id.org/cwl/view/git/d1ee6a2a323cee7e4af00c7e0b926c2192038e1d/rnaseq/bam_to_trimmed_fastq_and_hisat_alignments.cwl