Workflow: trim_and_map.cwl

Fetched 2020-02-22 16:18:39 GMT
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Inputs

ID Type Title Doc
max_mapping_insert_length Long (Optional)
genome File
adapter2 String (Optional)
adapter1 String (Optional)
fastq2 File (Optional)
fastq1 File
is_paired_end Boolean

Steps

ID Runs Label Doc
sam2bam
../tools/samtools_view_sam2bam.cwl (CommandLineTool)
mapping
../tools/bowtie2.cwl (CommandLineTool)
adaptor_trimming_and_qc_trimmed
../tools/trim_galore.cwl (CommandLineTool)
qc_raw
../tools/fastqc.cwl (CommandLineTool)
sort_bam
../tools/samtools_sort.cwl (CommandLineTool)

Sort a bam file by read names.

Outputs

ID Type Label Doc
bowtie2_log File
trim_galore_log File[]
trimmed_fastqc_zip File[]
fastq2_trimmed File (Optional)
trimmed_fastqc_html File[]
fastq1_trimmed File
raw_fastqc_html File[]
raw_fastqc_zip File[]
bam File
Permalink: https://w3id.org/cwl/view/git/7828cbb2c596936d386876ff84cb80c25b507713/CWL/workflow_modules/trim_and_map.cwl