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	79e049ced4dd9e6d0bb004d5f8c48169[]
raw_fastqc_html	842031a76d003404fe1241c6abb3209c[]
trim_galore_log	4651583b1c935d3452c4969b2e6b8c4d[]
duprem_fastqc_zip	File[]
qc_crosscorr_plot	File (Optional)
duprem_fastqc_html	File[]
picard_markdup_log	File
trimmed_fastqc_zip	22b5eb5b224819d0549a27ca7e10bbdf[]
trimmed_fastqc_html	be5d6db262f50e71d35b4cc800fe11f3[]
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)