Workflow: pipeline-pe-umis.cwl

Fetched 2021-01-09 04:27:50 GMT

STARR-seq pipeline - reads: PE

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Inputs

ID Type Title Doc
nthreads_qc Integer

Number of threads - qc.

nthreads_map Integer

Number of threads - map.

fgbio_jar_path String

fgbio Java jar file

nthreads_quant Integer

Number of threads - quantification.

nthreads_trimm Integer

Number of threads - trim.

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\")

regions_bed_file File

Regions bed file used to filter-in reads (used in samtools, for example chromosomes of interest)

genome_sizes_file File

Genome sizes tab-delimited file (used in samtools)

trimmomatic_jar_path String

Trimmomatic Java jar file

default_adapters_file File

Adapters file

input_fastq_umi_files File[]

Input fastq with UMIs files

trimmomatic_java_opts String (Optional)

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

input_fastq_read1_files File[]

Input read1 fastq files

input_fastq_read2_files File[]

Input read2 fastq files

ENCODE_blacklist_bedfile File

Bedfile containing ENCODE consensus blacklist regions to be excluded.

genome_ref_first_index_file File

\"First index file of Bowtie2 reference genome with extension 1.bt2. \ (Note: the rest of the index files MUST be in the same folder)\"

Steps

ID Runs Label Doc
qc
01-qc-pe.cwl (Workflow)

STARR-seq 01 QC - reads: PE

map
03-map-pe-umis.cwl (Workflow)

STARR-seq 03 mapping - reads: PE

trim
02-trim-pe.cwl (Workflow)

STARR-seq 02 trimming - reads: PE

quant

STARR-seq 04 quantification

Outputs

ID Type Label Doc
map_bowtie_log_files File[]

Bowtie log file with mapping stats

map_preseq_c_curve_files File[]

Preseq c_curve output files

map_unmapped_fastq_files File[]

Gzip compressed FASTQ ummaped and unpaired sequences

output_diff_counts_read1 File[]
output_diff_counts_read2 File[]
quant_bw_dedup_raw_files File[]

Signal files with 1bp raw read pileup ignoring duplicates.

map_dups_marked_bam_files File[]

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

map_mark_duplicates_files File[]

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

quant_bw_dedup_norm_files File[]

Signal files with RPKM normalization ignoring duplicates.

map_genomic_template_files File[]

BEDPE files with fragment/template coordinates

output_count_raw_reads_read1 File[]
output_count_raw_reads_read2 File[]
output_custom_adapters_read1 File[]
output_custom_adapters_read2 File[]
quant_bw_with_dups_norm_files File[]

Signal files with RPKM normalization including duplicates.

output_fastqc_data_files_read1 File[]

FastQC data files for paired read 1

output_fastqc_data_files_read2 File[]

FastQC data files for paired read 2

output_fastqc_report_files_read1 File[]

FastQC reports in zip format for paired read 1

output_fastqc_report_files_read2 File[]

FastQC reports in zip format for paired read 2

output_data_fastq_read1_trimmed_files File[]

Trimmed fastq files for paired read 1

output_data_fastq_read2_trimmed_files File[]

Trimmed fastq files for paired read 2

output_trimmed_read1_fastq_read_count File[]

Trimmed read counts of paired read 1 fastq files

output_trimmed_read2_fastq_read_count File[]

Trimmed read counts of paired read 2 fastq files

Permalink: https://w3id.org/cwl/view/git/4e568335133405d28f4b73ae11e7f51f2900dfa3/v1.0/STARR-seq_pipeline/pipeline-pe-umis.cwl