Workflow: pipeline-se-with-control.cwl

Fetched 2018-12-19 18:08:05 GMT

ChIP-seq pipeline - reads: SE, samples: treatment and control.

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Inputs

ID Type Title Doc
genome_sizes_file File

Genome sizes tab-delimited file (used in samtools)

as_broadPeak_file File

Definition broadPeak file in AutoSql format (used in bedToBigBed)

input_treatment_fastq_files File[]

Input treatment fastq files

trimmomatic_java_opts String (Optional)

JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")

nthreads_map Integer

Number of threads required for the 03-map step

nthreads_qc Integer

Number of threads required for the 01-qc step

nthreads_peakcall Integer

Number of threads required for the 04-peakcall step

input_control_fastq_files File[]

Input control fastq files

nthreads_trimm Integer

Number of threads required for the 02-trim step

trimmomatic_jar_path String

Trimmomatic Java jar 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

picard_java_opts String (Optional)

JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")

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)\"

picard_jar_path String

Picard Java jar file

ENCODE_blacklist_bedfile File

Bedfile containing ENCODE consensus blacklist regions to be excluded.

as_narrowPeak_file File

Definition narrowPeak file in AutoSql format (used in bedToBigBed)

default_adapters_file File

Adapters file

nthreads_quant Integer

Number of threads required for the 05-quantification step

Steps

ID Runs Label Doc
map_control
03-map-se.cwl (Workflow)

ChIP-seq 03 mapping - reads: SE

peak_call_control
04-peakcall.cwl (Workflow)

ChIP-seq 04 quantification - samples: treatment.

map_treatment
03-map-se.cwl (Workflow)

ChIP-seq 03 mapping - reads: SE

qc_control
01-qc-se.cwl (Workflow)

ChIP-seq 01 QC - reads: SE

peak_call_treatment

ChIP-seq 04 quantification - samples: treatment and control.

quant

ChIP-seq - Quantification - samples: treatment and control

trimm_control
02-trim-se.cwl (Workflow)

ChIP-seq 02 trimming - reads: SE

qc_treatment
01-qc-se.cwl (Workflow)

ChIP-seq 01 QC - reads: SE

trimm_treatment
02-trim-se.cwl (Workflow)

ChIP-seq 02 trimming - reads: SE

Outputs

ID Type Label Doc
peak_call_treatment_read_in_narrowpeak_count_within_replicate File[]

Peak counts within replicate

qc_control_diff_counts File[]

Diff file between number of raw reads and number of reads counted by FASTQC, for control

quant_bigwig_ctrl_subtracted_rpkm_extended_files File[]

Fragment control subtracted extended reads bigWig (signal) files

peak_call_control_narrowpeak_bigbed_file File[]

narrowPeaks in bigBed format

peak_call_treatment_narrowpeak_file File[]

Peaks in narrowPeak file format

peak_call_treatment_broadpeak_file File[]

Peaks in broadPeak file format

map_treatment_mark_duplicates_files File[]

Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions) for treatment

map_control_bowtie_log_files File[]

Bowtie log file with mapping stats for control

map_treatment_bowtie_log_files File[]

Bowtie log file with mapping stats for treatment

peak_call_control_read_in_broadpeak_count_within_replicate File[]

Peak counts within replicate

qc_control_fastqc_report_files File[]

FastQC report files

peak_call_control_read_in_narrowpeak_count_within_replicate File[]

Peak counts within replicate

peak_call_treatment_spp_x_cross_corr_plot File[]

SPP strand cross correlation plot

peak_call_control_filtered_read_count_file File[]

Filtered read count after peak calling

map_treatment_preseq_percentage_uniq_reads File[]

Preseq percentage of uniq reads

peak_call_control_broadpeak_count File[]

Peak counts within replicate

map_treatment_preseq_c_curve_files File[]

Preseq c_curve output files for treatment

peak_call_treatment_narrowpeak_bigbed_file File[]

narrowPeaks in bigBed format

map_control_preseq_c_curve_files File[]

Preseq c_curve output files for control

peak_call_control_narrowpeak_file File[]

Peaks in narrowPeak file format

peak_call_control_broadpeak_file File[]

Peaks in broadPeak file format

peak_call_control_spp_x_cross_corr_plot File[]

SPP strand cross correlation plot

trimm_control_fastq_files File[]

FASTQ files after trimming step for control

qc_treatment_count_raw_reads File[]

Raw read counts of fastq files after QC for treatment

peak_call_treatment_read_in_broadpeak_count_within_replicate File[]

Peak counts within replicate

map_control_dedup_bam_files File[]

Filtered BAM files (post-processing end point) for control

map_control_read_count_mapped File[]

Read counts of the mapped BAM files

qc_treatment_diff_counts File[]

Diff file between number of raw reads and number of reads counted by FASTQC, for treatment

map_control_mark_duplicates_files File[]

Summary of duplicates removed with Picard tool MarkDuplicates (for multiple reads aligned to the same positions) for control

quant_bigwig_rpkm_extended_files File[]

Fragment extended reads bigWig (signal) files

peak_call_treatment_broadpeak_bigbed_file File[]

broadPeaks in bigBed format

map_treatment_dedup_bam_files File[]

Filtered BAM files (post-processing end point) for treatment

quant_bigwig_raw_files File[]

Raw reads bigWig (signal) files

qc_treatment_fastqc_report_files File[]

FastQC report files

peak_call_treatment_narrowpeak_summits_file dc9418e813b5868c3f4ec97453092e0f[]

Peaks summits in bedfile format

peak_call_control_broadpeak_bigbed_file File[]

broadPeaks in bigBed format

peak_call_treatment_broadpeak_count File[]

Peak counts within replicate

qc_control_fastqc_data_files File[]

FastQC data files

trimm_treatment_fastq_files File[]

FASTQ files after trimming step for control

peak_call_control_narrowpeak_peak_xls_file File[]

Peak calling report file

map_treatment_read_count_mapped File[]

Read counts of the mapped BAM files

qc_control_count_raw_reads File[]

Raw read counts of fastq files after QC for control

trimm_treatment_raw_counts File[]

Raw read counts for fastq files after trimming for treatment

peak_call_control_narrowpeak_summits_file d92561ee5ceb163c8d7e698500274c9c[]

Peaks summits in bedfile format

peak_call_treatment_narrowpeak_peak_xls_file File[]

Peak calling report file

map_treatment_dups_marked_bam_files File[]

Filtered BAM files with duplicates marked (post-processing end point) for treatment

quant_ctrl_bigwig_rpkm_extended_files File[]

Fragment extended reads bigWig (signal) control files

peak_call_control_spp_x_cross_corr File[]

SPP strand cross correlation summary

peak_call_control_narrowpeak_count File[]

Peak counts within replicate

trimm_control_raw_counts File[]

Raw read counts for fastq files after trimming for control

map_control_dups_marked_bam_files File[]

Filtered BAM files with duplicates marked (post-processing end point) for control

peak_call_treatment_filtered_read_count_file File[]

Filtered read count after peak calling

peak_call_treatment_narrowpeak_count File[]

Peak counts within replicate

qc_treatment_fastqc_data_files File[]

FastQC data files

map_treatment_pbc_files File[]

PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5) for control

peak_call_treatment_spp_x_cross_corr File[]

SPP strand cross correlation summary

map_control_pbc_files File[]

PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5) for control

map_control_preseq_percentage_uniq_reads File[]

Preseq percentage of uniq reads

Permalink: https://w3id.org/cwl/view/git/6d9457382f0b7cc2510e148d21383261280d17ed/v1.0/ChIP-seq_pipeline/pipeline-se-with-control.cwl