CWL Workflow: pipeline-pe-blacklist-removal.cwl

Workflow: pipeline-pe-blacklist-removal.cwl

Fetched 2023-01-04 07:24:29 GMT

Verified with cwltool version 3.1.20221201130942

ATAC-seq pipeline - reads: PE - with blacklist removal

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Default Values
Nested Workflows
Tools
Inputs/Outputs

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

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

Inputs

ID	Type	Doc
nthreads_qc	Integer	Number of threads required for the 01-qc step
nthreads_map	Integer	Number of threads required for the 03-map step
nthreads_quant	Integer	Number of threads required for the 05-quantification step
nthreads_trimm	Integer	Number of threads required for the 02-trim step
picard_jar_path	String	Picard Java jar file
picard_java_opts	String (Optional)	JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")
genome_sizes_file	File	Genome sizes tab-delimited file (used in samtools)
nthreads_peakcall	Integer	Number of threads required for the 04-peakcall step
as_narrowPeak_file	File	Definition narrowPeak file in AutoSql format (used in bedToBigBed)
trimmomatic_jar_path	String	Trimmomatic Java jar file
default_adapters_file	File	Adapters file
genome_effective_size	String	Effective genome size used by MACS2. It can be numeric or a shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8), Default:hs
trimmomatic_java_opts	String (Optional)	JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")
input_fastq_read1_files	File[]	Input fastq paired-end read 1 files
input_fastq_read2_files	File[]	Input fastq paired-end read 2 files
ENCODE_blacklist_bedfile	File	Bedfile containing ENCODE consensus blacklist regions to be excluded.
genome_ref_first_index_file	File	\"First index file of Bowtie reference genome with extension 1.ebwt. \ (Note: the rest of the index files MUST be in the same folder)\"

Steps

ID	Runs	Doc
qc	01-qc-pe.cwl (Workflow)	ATAC-seq 01 QC - reads: PE
map	03-map-pe-blacklist-removal.cwl (Workflow)	ATAC-seq 03 mapping - reads: PE - blacklist removal
quant	05-quantification.cwl (Workflow)	ATAC-seq - Quantification
trimm	02-trim-pe.cwl (Workflow)	ATAC-seq 02 trimming - reads: PE
peak_call	04-peakcall-pe.cwl (Workflow)	ATAC-seq 04 quantification - PE

Outputs

ID	Type	Doc
map_pbc_files	File[]	PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)
peakcall_peak_file	File[]	Peaks in ENCODE Peak file format
map_dedup_bam_files	File[]	Filtered BAM files (post-processing end point)
map_bowtie_log_files	File[]	Bowtie log file with mapping stats
qc_diff_counts_read1	File[]	Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read1
qc_diff_counts_read2	File[]	Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read2
map_read_count_mapped	File[]	Read counts of the mapped BAM files
peakcall_peak_xls_file	File[]	Peak calling report file
quant_bigwig_raw_files	File[]	Raw reads bigWig (signal) files
trimm_raw_counts_read1	File[]	Raw read counts for paired_read1 of fastq files after trimming
trimm_raw_counts_read2	File[]	Raw read counts for paired_read2 of fastq files after trimming
quant_bigwig_norm_files	File[]	Normalized reads bigWig (signal) files
trimm_fastq_files_read1	File[]	FASTQ files for paired_read1 after trimming
trimm_fastq_files_read2	File[]	FASTQ files for paired_read2 after trimming
map_preseq_c_curve_files	File[]	Preseq c_curve output files
qc_count_raw_reads_read1	File[]	Raw read counts of fastq files for paired_read1 after QC
qc_count_raw_reads_read2	File[]	Raw read counts of fastq files for paired_read2 after QC
map_mark_duplicates_files	File[]	Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions
peakcall_peak_bigbed_file	File[]	Peaks in bigBed format
peakcall_spp_x_cross_corr	File[]	SPP strand cross correlation summary
peakcall_peak_summits_file	File[]	Peaks summits in bedfile format
qc_fastqc_data_files_read1	File[]	FastQC data files for paired_read1
qc_fastqc_data_files_read2	File[]	FastQC data files for paired_read2
peakcall_extended_peak_file	File[]	Extended fragment peaks in ENCODE Peak file format
qc_fastqc_report_files_read1	File[]	FastQC reports in zip format for paired_read1
qc_fastqc_report_files_read2	File[]	FastQC reports in zip format for paired_read2
peakcall_spp_x_cross_corr_plot	File[]	SPP strand cross correlation plot
map_percent_mitochondrial_reads	File[]	Percentage of mitochondrial reads
map_preseq_percentage_uniq_reads	File[]	Preseq percentage of uniq reads
peakcall_filtered_read_count_file	File[]	Filtered read count after peak calling
peakcall_output_unpaired_peak_file	File[]	peakshift/phantomPeak results file using each paired mate independently
peakcall_peak_count_within_replicate	File[]	Peak counts within replicate
peakcall_output_unpaired_peak_xls_file	File[]	Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently
peakcall_output_unpaired_peak_bigbed_file	File[]	peakshift/phantomPeak results bigbed file using each paired mate independently
peakcall_output_unpaired_peak_summits_file	File[]	File containing peak summits using each paired mate independently
peakcall_output_unpaired_extended_peak_file	File[]	peakshift/phantomPeak extended fragment results file using each paired mate independently
peakcall_read_in_peak_count_within_replicate	File[]	Peak counts within replicate
peakcall_output_unpaired_filtered_read_count_file	File[]	Filtered read count reported by MACS2 using each paired mate independently
peakcall_output_unpaired_peak_count_within_replicate	File[]	Peak counts within replicate using each paired mate independently

Permalink:

https://w3id.org/cwl/view/git/517487e59d240c197fc91f08d20dadca97a9e121/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl