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|
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: ATAC-seq-pipeline-se
doc: 'ATAC-seq pipeline - reads: SE'
$namespaces:
sbg: https://sevenbridges.com
requirements:
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
as_narrowPeak_file:
doc: Definition narrowPeak file in AutoSql format (used in bedToBigBed)
type: File
default_adapters_file:
doc: Adapters file
type: File
genome_effective_size:
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
default: hs
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
genome_sizes_file:
doc: Genome sizes tab-delimited file (used in samtools)
type: File
input_fastq_files:
type: File[]
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_qc:
doc: Number of threads required for the 01-qc step
type: int
nthreads_quant:
doc: Number of threads required for the 05-quantification step
type: int
nthreads_trimm:
doc: Number of threads required for the 02-trim step
type: int
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?
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?
outputs:
map_bowtie_log_files:
doc: Bowtie log file with mapping stats
type: File[]
outputSource: map/output_bowtie_log
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_pbc_files:
doc: PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)
type: File[]
outputSource: map/output_pbc_files
map_percent_mitochondrial_reads:
doc: Percentage of mitochondrial reads
type: File[]
outputSource: map/output_percent_mitochondrial_reads
map_preseq_c_curve_files:
doc: Preseq c_curve output files
type: File[]
outputSource: map/output_preseq_c_curve_files
map_preseq_percentage_uniq_reads:
doc: Preseq percentage of uniq reads
type: File[]
outputSource: map/output_percentage_uniq_reads
map_read_count_mapped:
doc: Read counts of the mapped BAM files
type: File[]
outputSource: map/output_read_count_mapped
peakcall_extended_peak_file:
doc: Extended fragment peaks in ENCODE Peak file format
type: File[]
outputSource: peak_call/output_extended_peak_file
peakcall_filtered_read_count_file:
doc: Filtered read count after peak calling
type: File[]
outputSource: peak_call/output_filtered_read_count_file
peakcall_peak_bigbed_file:
doc: Peaks in bigBed format
type: File[]
outputSource: peak_call/output_peak_bigbed_file
peakcall_peak_count_within_replicate:
doc: Peak counts within replicate
type: File[]
outputSource: peak_call/output_peak_count_within_replicate
peakcall_peak_file:
doc: Peaks in ENCODE Peak file format
type: File[]
outputSource: peak_call/output_peak_file
peakcall_peak_summits_file:
doc: Peaks summits in bedfile format
type: File[]
outputSource: peak_call/output_peak_summits_file
peakcall_peak_xls_file:
doc: Peak calling report file
type: File[]
outputSource: peak_call/output_peak_xls_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_spp_x_cross_corr:
doc: SPP strand cross correlation summary
type: File[]
outputSource: peak_call/output_spp_x_cross_corr
peakcall_spp_x_cross_corr_plot:
doc: SPP strand cross correlation plot
type: File[]
outputSource: peak_call/output_spp_cross_corr_plot
qc_count_raw_reads:
doc: Raw read counts of fastq files after QC
type: File[]
outputSource: qc/output_count_raw_reads
qc_diff_counts:
doc: Diff file between number of raw reads and number of reads counted by FASTQC,
type: File[]
outputSource: qc/output_diff_counts
qc_fastqc_data_files:
doc: FastQC data files
type: File[]
outputSource: qc/output_fastqc_data_files
qc_fastqc_report_files:
doc: FastQC reports in zip format
type: File[]
outputSource: qc/output_fastqc_report_files
quant_bigwig_norm_files:
doc: Normalized reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_norm_files
quant_bigwig_raw_files:
doc: Raw reads bigWig (signal) files
type: File[]
outputSource: quant/bigwig_raw_files
trimm_fastq_files:
doc: FASTQ files after trimming
type: File[]
outputSource: trimm/output_data_fastq_trimmed_files
trimm_raw_counts:
doc: Raw read counts of fastq files after trimming
type: File[]
outputSource: trimm/output_trimmed_fastq_read_count
steps:
map:
in:
genome_ref_first_index_file: genome_ref_first_index_file
genome_sizes_file: genome_sizes_file
input_fastq_files: trimm/output_data_fastq_trimmed_files
nthreads: nthreads_map
picard_jar_path: picard_jar_path
picard_java_opts: picard_java_opts
run: expected-exploded-atac-seq.cwl.steps/map.cwl
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:
in:
as_narrowPeak_file: as_narrowPeak_file
genome_effective_size: genome_effective_size
input_bam_files: map/output_data_sorted_dedup_bam_files
input_bam_format:
valueFrom: BAM
input_genome_sizes: genome_sizes_file
nthreads: nthreads_peakcall
run: expected-exploded-atac-seq.cwl.steps/peak_call.cwl
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
qc:
in:
default_adapters_file: default_adapters_file
input_fastq_files: input_fastq_files
nthreads: nthreads_qc
run: expected-exploded-atac-seq.cwl.steps/qc.cwl
out:
- output_count_raw_reads
- output_diff_counts
- output_fastqc_report_files
- output_fastqc_data_files
- output_custom_adapters
quant:
in:
input_bam_files: map/output_data_sorted_dedup_bam_files
input_genome_sizes: genome_sizes_file
nthreads: nthreads_quant
run: expected-exploded-atac-seq.cwl.steps/quant.cwl
out:
- bigwig_raw_files
- bigwig_norm_files
trimm:
in:
input_adapters_files: qc/output_custom_adapters
input_fastq_files: input_fastq_files
nthreads: nthreads_trimm
trimmomatic_jar_path: trimmomatic_jar_path
trimmomatic_java_opts: trimmomatic_java_opts
run: expected-exploded-atac-seq.cwl.steps/trimm.cwl
out:
- output_data_fastq_trimmed_files
- output_trimmed_fastq_read_count
id: |-
https://api.sbgenomics.com/v2/apps/kghosesbg/sbpla-31744/ATAC-seq-pipeline-se/2/raw/
sbg:appVersion:
- v1.0
sbg:content_hash: ad9474546d1d7aba5aa20e3c7a03b5429e5f8ec1d18be92cbab7315600a6bce48
sbg:contributors:
- kghosesbg
sbg:createdBy: kghosesbg
sbg:createdOn: 1580500895
sbg:id: kghosesbg/sbpla-31744/ATAC-seq-pipeline-se/2
sbg:image_url: |-
https://igor.sbgenomics.com/ns/brood/images/kghosesbg/sbpla-31744/ATAC-seq-pipeline-se/2.png
sbg:latestRevision: 2
sbg:modifiedBy: kghosesbg
sbg:modifiedOn: 1581699121
sbg:project: kghosesbg/sbpla-31744
sbg:projectName: SBPLA-31744
sbg:publisher: sbg
sbg:revision: 2
sbg:revisionNotes: |-
Uploaded using sbpack v2020.02.14.
Source: https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl
sbg:revisionsInfo:
- sbg:modifiedBy: kghosesbg
sbg:modifiedOn: 1580500895
sbg:revision: 0
sbg:revisionNotes: |-
Uploaded using sbpack. Source: https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl
- sbg:modifiedBy: kghosesbg
sbg:modifiedOn: 1580742764
sbg:revision: 1
sbg:revisionNotes: Just moved a node
- sbg:modifiedBy: kghosesbg
sbg:modifiedOn: 1581699121
sbg:revision: 2
sbg:revisionNotes: |-
Uploaded using sbpack v2020.02.14.
Source: https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl
sbg:sbgMaintained: false
sbg:validationErrors:
- 'Required input is not set: #qc.input_fastq_files'
- 'Required input is not set: #qc.default_adapters_file'
- 'Required input is not set: #qc.nthreads'
- 'Required input is not set: #trimm.input_fastq_files'
- 'Required input is not set: #trimm.input_adapters_files'
- 'Required input is not set: #map.input_fastq_files'
- 'Required input is not set: #map.genome_sizes_file'
- 'Required input is not set: #map.genome_ref_first_index_file'
- 'Required input is not set: #peak_call.input_bam_files'
- 'Required input is not set: #peak_call.input_genome_sizes'
- 'Required input is not set: #peak_call.as_narrowPeak_file'
- 'Required input is not set: #quant.input_bam_files'
- 'Required input is not set: #quant.input_genome_sizes'
|
