Workflow: pipeline-se-blacklist-removal.cwl

Fetched 2024-04-23 04:10:00 GMT

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

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Inputs

ID Type Title 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)

input_fastq_files File[]
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\")

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 Label Doc
qc
01-qc-se.cwl (Workflow)

ATAC-seq 01 QC - reads: SE

map

ATAC-seq 03 mapping - reads: SE - blacklist removal

quant

ATAC-seq - Quantification

trimm
02-trim-se.cwl (Workflow)

ATAC-seq 02 trimming - reads: SE

peak_call
04-peakcall-se.cwl (Workflow)

ATAC-seq 04 quantification - SE

Outputs

ID Type Label Doc
map_pbc_files File[]

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

qc_diff_counts File[]

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

trimm_raw_counts File[]

Raw read counts of fastq files after trimming

trimm_fastq_files File[]

FASTQ files after trimming

peakcall_peak_file File[]

Peaks in ENCODE Peak file format

qc_count_raw_reads File[]

Raw read counts of fastq files after QC

map_dedup_bam_files File[]

Filtered BAM files (post-processing end point)

map_bowtie_log_files File[]

Bowtie log file with mapping stats

qc_fastqc_data_files File[]

FastQC data files

map_read_count_mapped File[]

Read counts of the mapped BAM files

peakcall_peak_xls_file File[]

Peak calling report file

qc_fastqc_report_files File[]

FastQC reports in zip format

quant_bigwig_raw_files File[]

Raw reads bigWig (signal) files

quant_bigwig_norm_files File[]

Normalized reads bigWig (signal) files

map_preseq_c_curve_files File[]

Preseq c_curve output files

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

peakcall_extended_peak_file File[]

Extended fragment peaks in ENCODE Peak file format

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_peak_count_within_replicate File[]

Peak counts within replicate

peakcall_read_in_peak_count_within_replicate File[]

Peak counts within replicate

Permalink: https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/pipeline-se-blacklist-removal.cwl