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pipeline-se.cwl
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pipeline-se.cwl
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class: Workflow
cwlVersion: v1.0
doc: 'DNase-seq pipeline - reads: SE'
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
inputs:
genome_sizes_file:
doc: Genome sizes tab-delimited file (used in samtools)
type: File
default_adapters_file:
doc: Adapters file
type: File
nthreads_quant:
doc: Number of threads required for the 05-quantification step
type: int
nthreads_peakcall:
doc: Number of threads required for the 04-peakcall step
type: int
input_fastq_files:
type: File[]
ENCODE_blacklist_bedfile:
doc: Bedfile containing ENCODE consensus blacklist regions to be excluded.
type: File
nthreads_map:
doc: Number of threads required for the 03-map step
type: int
genome_ref_first_index_file:
doc: '"First index file of Bowtie reference genome with extension 1.ebwt. \ (Note: the rest of the index files MUST be in the same folder)" '
type: File
steps:
map:
in:
genome_sizes_file: genome_sizes_file
ENCODE_blacklist_bedfile: ENCODE_blacklist_bedfile
genome_ref_first_index_file: genome_ref_first_index_file
nthreads: nthreads_map
input_fastq_files: input_fastq_files
run: 01-map-se.cwl
out:
- output_data_filtered_bam_files
- output_pbc_files
- output_bowtie_log
- output_preseq_c_curve_files
- original_fastq_read_count
- output_read_count_mapped
- output_read_count_mapped_filtered
- output_percentage_uniq_reads
quant:
in:
nthreads: nthreads_quant
input_pileup_bedgraphs: peak_call/output_extended_narrowpeak_file
input_bam_files: map/output_data_filtered_bam_files
input_peak_xls_files: peak_call/output_peak_xls_file
input_read_count_dedup_files: peak_call/output_read_in_peak_count_within_replicate
input_genome_sizes: genome_sizes_file
run: 03-quantification.cwl
out:
- bigwig_raw_files
- bigwig_norm_files
- bigwig_extended_files
- bigwig_extended_norm_files
peak_call:
in:
input_bam_format:
valueFrom: BAM
input_bam_files: map/output_data_filtered_bam_files
nthreads: nthreads_peakcall
run: 02-peakcall.cwl
out:
- output_spp_x_cross_corr
- output_spp_cross_corr_plot
- output_narrowpeak_file
- output_extended_narrowpeak_file
- output_peak_xls_file
- output_filtered_read_count_file
- output_peak_count_within_replicate
- output_read_in_peak_count_within_replicate
outputs:
quant_bigwig_raw_files:
doc: Raw reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_raw_files
quant_bigwig_extended_files:
doc: Fragment extended reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_extended_files
map_preseq_c_curve_files:
doc: Preseq c_curve output files
type: File[]
outputSource: map/output_preseq_c_curve_files
map_percentage_uniq_reads:
doc: Percentage of uniq reads from preseq c_curve output
type: File[]
outputSource: map/output_percentage_uniq_reads
peak_call_spp_x_cross_corr:
doc: SPP strand cross correlation summary
type: File[]
outputSource: peak_call/output_spp_x_cross_corr
peak_call_peak_xls_file:
doc: Peak calling report file
type: File[]
outputSource: peak_call/output_peak_xls_file
map_filtered_bam_files:
doc: Filtered BAM files (post-processing end point)
type: File[]
outputSource: map/output_data_filtered_bam_files
peak_call_extended_narrowpeak_file:
doc: Extended fragment peaks in narrowPeak file format
type: File[]
outputSource: peak_call/output_extended_narrowpeak_file
peak_call_read_in_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: peak_call/output_read_in_peak_count_within_replicate
quant_bigwig_extended_norm_files:
doc: Normalized fragment extended reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_extended_norm_files
map_bowtie_log_files:
doc: Bowtie log file with mapping stats
type: File[]
outputSource: map/output_bowtie_log
map_pbc_files:
doc: PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)
type: File[]
outputSource: map/output_pbc_files
map_filtered_read_count:
doc: Read counts of the mapped and filtered BAM files
type: File[]
outputSource: map/output_read_count_mapped_filtered
peak_call_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: peak_call/output_peak_count_within_replicate
fastq_read_count:
doc: Read counts of the (unprocessed) input fastq files
type: File[]
outputSource: map/original_fastq_read_count
peak_call_narrowpeak_file:
doc: Peaks in narrowPeak file format
type: File[]
outputSource: peak_call/output_narrowpeak_file
peak_call_spp_x_cross_corr_plot:
doc: SPP strand cross correlation plot
type: File[]
outputSource: peak_call/output_spp_cross_corr_plot
peak_call_filtered_read_count_file:
doc: Filtered read count after peak calling
type: File[]
outputSource: peak_call/output_filtered_read_count_file
map_read_count:
doc: Read counts of the mapped BAM files
type: File[]
outputSource: map/output_read_count_mapped
quant_bigwig_norm_files:
doc: Normalized reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_norm_files