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pipeline-pe.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
doc: 'ATAC-seq pipeline - reads: PE'
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
input_fastq_read1_files:
doc: Input fastq paired-end read 1 files
type: File[]
input_fastq_read2_files:
doc: Input fastq paired-end read 2 files
type: File[]
genome_sizes_file:
doc: Genome sizes tab-delimited file (used in samtools)
type: File
default_adapters_file:
doc: Adapters file
type: File
genome_effective_size:
default: hs
doc: 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
type: string
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
secondaryFiles:
- ^^.2.ebwt
- ^^.3.ebwt
- ^^.4.ebwt
- ^^.rev.1.ebwt
- ^^.rev.2.ebwt
as_narrowPeak_file:
doc: Definition narrowPeak file in AutoSql format (used in bedToBigBed)
type: File
trimmomatic_jar_path:
doc: Trimmomatic Java jar file
type: string
trimmomatic_java_opts:
doc: JVM arguments should be a quoted, space separated list (e.g. "-Xms128m -Xmx512m")
type: string?
picard_jar_path:
doc: Picard Java jar file
type: string
picard_java_opts:
doc: JVM arguments should be a quoted, space separated list (e.g. "-Xms128m -Xmx512m")
type: string?
nthreads_qc:
doc: Number of threads required for the 01-qc step
type: int
nthreads_trimm:
doc: Number of threads required for the 02-trim step
type: int
nthreads_map:
doc: Number of threads required for the 03-map step
type: int
nthreads_peakcall:
doc: Number of threads required for the 04-peakcall step
type: int
nthreads_quant:
doc: Number of threads required for the 05-quantification step
type: int
steps:
qc:
run: 01-qc-pe.cwl
in:
input_read1_fastq_files: input_fastq_read1_files
input_read2_fastq_files: input_fastq_read2_files
default_adapters_file: default_adapters_file
nthreads: nthreads_qc
out:
- output_count_raw_reads_read1
- output_diff_counts_read1
- output_fastqc_report_files_read1
- output_fastqc_data_files_read1
- output_custom_adapters_read1
- output_count_raw_reads_read2
- output_diff_counts_read2
- output_fastqc_report_files_read2
- output_fastqc_data_files_read2
- output_custom_adapters_read2
trimm:
run: 02-trim-pe.cwl
in:
input_read1_fastq_files: input_fastq_read1_files
input_read1_adapters_files: qc/output_custom_adapters_read1
input_read2_fastq_files: input_fastq_read2_files
input_read2_adapters_files: qc/output_custom_adapters_read2
trimmomatic_jar_path: trimmomatic_jar_path
trimmomatic_java_opts: trimmomatic_java_opts
nthreads: nthreads_trimm
out:
- output_data_fastq_read1_trimmed_files
- output_trimmed_read1_fastq_read_count
- output_data_fastq_read2_trimmed_files
- output_trimmed_read2_fastq_read_count
map:
run: 03-map-pe.cwl
in:
input_fastq_read1_files: trimm/output_data_fastq_read1_trimmed_files
input_fastq_read2_files: trimm/output_data_fastq_read2_trimmed_files
genome_sizes_file: genome_sizes_file
genome_ref_first_index_file: genome_ref_first_index_file
picard_jar_path: picard_jar_path
picard_java_opts: picard_java_opts
nthreads: nthreads_map
out:
- output_data_sorted_dedup_bam_files
- output_data_sorted_dups_marked_bam_files
- output_picard_mark_duplicates_files
- output_pbc_files
- output_bowtie_log
- output_preseq_c_curve_files
- output_percentage_uniq_reads
- output_read_count_mapped
- output_percent_mitochondrial_reads
peak_call:
run: 04-peakcall-pe.cwl
in:
input_bam_files: map/output_data_sorted_dedup_bam_files
input_bam_format:
valueFrom: BAMPE
genome_effective_size: genome_effective_size
input_genome_sizes: genome_sizes_file
as_narrowPeak_file: as_narrowPeak_file
nthreads: nthreads_peakcall
out:
- output_spp_x_cross_corr
- output_spp_cross_corr_plot
- output_read_in_peak_count_within_replicate
- output_peak_file
- output_peak_bigbed_file
- output_peak_summits_file
- output_extended_peak_file
- output_peak_xls_file
- output_filtered_read_count_file
- output_peak_count_within_replicate
- output_unpaired_peak_file
- output_unpaired_peak_bigbed_file
- output_unpaired_peak_summits_file
- output_unpaired_extended_peak_file
- output_unpaired_peak_xls_file
- output_unpaired_filtered_read_count_file
- output_unpaired_peak_count_within_replicate
quant:
run: 05-quantification.cwl
in:
input_bam_files: map/output_data_sorted_dedup_bam_files
input_genome_sizes: genome_sizes_file
nthreads: nthreads_quant
out:
- bigwig_raw_files
- bigwig_norm_files
outputs:
qc_fastqc_data_files_read1:
doc: FastQC data files for paired_read1
type: File[]
outputSource: qc/output_fastqc_data_files_read1
qc_fastqc_report_files_read1:
doc: FastQC reports in zip format for paired_read1
type: File[]
outputSource: qc/output_fastqc_report_files_read1
qc_count_raw_reads_read1:
doc: Raw read counts of fastq files for paired_read1 after QC
type: File[]
outputSource: qc/output_count_raw_reads_read1
qc_diff_counts_read1:
doc: Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read1
type: File[]
outputSource: qc/output_diff_counts_read1
trimm_fastq_files_read1:
doc: FASTQ files for paired_read1 after trimming
type: File[]
outputSource: trimm/output_data_fastq_read1_trimmed_files
trimm_raw_counts_read1:
doc: Raw read counts for paired_read1 of fastq files after trimming
type: File[]
outputSource: trimm/output_trimmed_read1_fastq_read_count
qc_fastqc_data_files_read2:
doc: FastQC data files for paired_read2
type: File[]
outputSource: qc/output_fastqc_data_files_read2
qc_fastqc_report_files_read2:
doc: FastQC reports in zip format for paired_read2
type: File[]
outputSource: qc/output_fastqc_report_files_read2
qc_count_raw_reads_read2:
doc: Raw read counts of fastq files for paired_read2 after QC
type: File[]
outputSource: qc/output_count_raw_reads_read2
qc_diff_counts_read2:
doc: Diff file between number of raw reads and number of reads counted by FASTQC, for paired_read2
type: File[]
outputSource: qc/output_diff_counts_read2
trimm_fastq_files_read2:
doc: FASTQ files for paired_read2 after trimming
type: File[]
outputSource: trimm/output_data_fastq_read2_trimmed_files
trimm_raw_counts_read2:
doc: Raw read counts for paired_read2 of fastq files after trimming
type: File[]
outputSource: trimm/output_trimmed_read2_fastq_read_count
map_read_count_mapped:
doc: Read counts of the mapped BAM files
type: File[]
outputSource: map/output_read_count_mapped
map_bowtie_log_files:
doc: Bowtie log file with mapping stats
type: File[]
outputSource: map/output_bowtie_log
map_preseq_percentage_uniq_reads:
doc: Preseq percentage of uniq reads
type: File[]
outputSource: map/output_percentage_uniq_reads
map_pbc_files:
doc: PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)
type: File[]
outputSource: map/output_pbc_files
map_dedup_bam_files:
doc: Filtered BAM files (post-processing end point)
type: File[]
outputSource: map/output_data_sorted_dups_marked_bam_files
map_mark_duplicates_files:
doc: Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions
type: File[]
outputSource: map/output_picard_mark_duplicates_files
map_preseq_c_curve_files:
doc: Preseq c_curve output files
type: File[]
outputSource: map/output_preseq_c_curve_files
map_percent_mitochondrial_reads:
doc: Percentage of mitochondrial reads
type: File[]
outputSource: map/output_percent_mitochondrial_reads
peakcall_peak_file:
doc: Peaks in ENCODE Peak file format
type: File[]
outputSource: peak_call/output_peak_file
peakcall_spp_x_cross_corr:
doc: SPP strand cross correlation summary
type: File[]
outputSource: peak_call/output_spp_x_cross_corr
peakcall_peak_xls_file:
doc: Peak calling report file
type: File[]
outputSource: peak_call/output_peak_xls_file
peakcall_peak_summits_file:
doc: Peaks summits in bedfile format
type: File[]
outputSource: peak_call/output_peak_summits_file
peakcall_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: peak_call/output_peak_count_within_replicate
peakcall_spp_x_cross_corr_plot:
doc: SPP strand cross correlation plot
type: File[]
outputSource: peak_call/output_spp_cross_corr_plot
peakcall_filtered_read_count_file:
doc: Filtered read count after peak calling
type: File[]
outputSource: peak_call/output_filtered_read_count_file
peakcall_extended_peak_file:
doc: Extended fragment peaks in ENCODE Peak file format
type: File[]
outputSource: peak_call/output_extended_peak_file
peakcall_read_in_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: peak_call/output_read_in_peak_count_within_replicate
peakcall_peak_bigbed_file:
doc: Peaks in bigBed format
type: File[]
outputSource: peak_call/output_peak_bigbed_file
peakcall_output_unpaired_peak_xls_file:
doc: Peak calling report file (*_peaks.xls file produced by MACS2) using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_peak_xls_file
peakcall_output_unpaired_extended_peak_file:
doc: peakshift/phantomPeak extended fragment results file using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_extended_peak_file
peakcall_output_unpaired_peak_count_within_replicate:
doc: Peak counts within replicate using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_peak_count_within_replicate
peakcall_output_unpaired_peak_bigbed_file:
doc: peakshift/phantomPeak results bigbed file using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_peak_bigbed_file
peakcall_output_unpaired_peak_file:
doc: peakshift/phantomPeak results file using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_peak_file
peakcall_output_unpaired_peak_summits_file:
doc: File containing peak summits using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_peak_summits_file
peakcall_output_unpaired_filtered_read_count_file:
doc: Filtered read count reported by MACS2 using each paired mate independently
type: File[]
outputSource: peak_call/output_unpaired_filtered_read_count_file
quant_bigwig_raw_files:
doc: Raw reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_raw_files
quant_bigwig_norm_files:
doc: Normalized reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_norm_files