CWL Workflow: ChIPseq_pipeline.cwl

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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
trim_galore_log	87ad9344b1a062684f58656811e15329[]
qc_crosscorr_plot	File (Optional)
pre_trim_fastqc_zip	47041ecff00eba1948693b264720ab77[]
post_trim_fastqc_zip	b1c54484e68e7f3a705162bc9d075061[]
pre_trim_fastqc_html	7e6d4f92de3808e43ee8ab0b246a5f69[]
qc_crosscorr_summary	File (Optional)
qc_plot_coverage_tsv	File
picard_markdup_stdout	File
post_trim_fastqc_html	7863a30d3602deb41f7a4f590644bf62[]
qc_plot_coverage_plot	File
post_filter_fastqc_zip	File[]
post_filter_fastqc_html	File[]
qc_plot_fingerprint_tsv	File (Optional)
qc_plot_fingerprint_plot	File (Optional)
qc_plot_fingerprint_stderr	File
qc_phantompeakqualtools_stderr	File (Optional)