CWL Workflow: ChIPseq_pipeline.cwl

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
fastq1	File[]
fastq2	File[]
adapter1	String[]
adapter2	String[]
bin_size	Integer (Optional)
reference	File
sample_id	String
fragment_size	Integer (Optional)
is_paired_end	Boolean
effective_genome_size	Long
ignoreForNormalization	String[]

ID	Runs	Label	Doc
chip_qc	../workflow_modules/chip_qc.cwl (Workflow)
trim_and_map	../workflow_modules/trim_and_map.cwl (Workflow)
merge_duprem_filter	../workflow_modules/merge_duprem_filter.cwl (Workflow)
create_summary_qc_report	../tools/multiqc_hack.cwl (CommandLineTool)
generate_coverage_tracks	../tools/deeptools_bamCoverage.cwl (CommandLineTool)

ID	Type	Label	Doc
bam	File
bigwig	File
bowtie2_log	File[]
multiqc_zip	File
multiqc_html	File
raw_fastqc_zip	bff26bd856a48952f6fb0b522b2dd749[]
raw_fastqc_html	cc85fc73837149a57366ba233e886d7f[]
trim_galore_log	69983726ef023fb1d50afa4370712d29[]
duprem_fastqc_zip	File[]
qc_crosscorr_plot	File (Optional)
duprem_fastqc_html	File[]
picard_markdup_log	File
trimmed_fastqc_zip	d686a6a96886b78daaad867fbb874665[]
trimmed_fastqc_html	8faf47bc071a34823d7bb3ff715ddda5[]
qc_crosscorr_summary	File (Optional)
qc_plot_coverage_tsv	File
qc_plot_coverage_plot	File
qc_plot_fingerprint_tsv	File (Optional)
qc_plot_fingerprint_plot	File (Optional)
qc_plot_fingerprint_stderr	File
qc_phantompeakqualtools_stderr	File (Optional)