Workflow: biowardrobe_chipseq_se.cwl

Fetched 2025-05-05 23:51:58 GMT

Current workflow is used to run CHIP-Seq basic analysis with single-end input FASTQ file. In outputs it returns coordinate sorted BAM file alongside with index BAI file, quality statistics of the input FASTQ file, reads coverage in a form of BigWig file, peaks calling data in a form of narrowPeak or broadPeak files.

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Inputs

ID Type Title Doc
threads Integer (Optional) Threads

Number of threads for those steps that support multithreading
broad_peak Boolean Callpeak broad

Set to call broad peak for MACS2
clip_3p_end Integer Clip from 3p end

Number of bases to clip from the 3p end
clip_5p_end Integer Clip from 5p end

Number of bases to clip from the 5p end
genome_size String Effective genome size

MACS2 effective genome size: hs, mm, ce, dm or number, for example 2.7e9
chrom_length File [Textual format] Chromosome length file

Chromosome length file
control_file File (Optional) [BAM] Control BAM file

Control BAM file file for MACS2 peak calling
fastq_input_file File [FASTQ] FASTQ input file

Reads data in a FASTQ format, received after single end sequencing
exp_fragment_size Integer Expected fragment size

Expected fragment size for MACS2
remove_duplicates Boolean Remove duplicates

Calls samtools rmdup to remove duplicates from sortesd BAM file
force_fragment_size Boolean Force fragment size

Force MACS2 to use exp_fragment_size
bowtie_indices_folder Directory BOWTIE indices folder

Path to BOWTIE generated indices folder

Steps

ID Runs Label Doc
get_stat
tools/python-get-stat.cwl (CommandLineTool)

Tool to process and combine log files generated by Bowtie aligner and samtools rmdup.

bam_to_bigwig

creates genome coverage bigWig file from .bam file
bamtools_stats
tools/bamtools-stats.cwl (CommandLineTool)

Tool is used to calculate general alignment statistics from the input BAM file

bowtie_aligner
tools/bowtie.cwl (CommandLineTool)

Tool is used to run bowtie aligner to align input FASTQ file(s) to reference genome

macs2_callpeak
tools/macs2-callpeak.cwl (CommandLineTool)

Tool is used to perform peak calling using MACS2. Input Trigger (default: true) allows to skip all calculation and return all input files unchanged. To set files to be returned in case of Trigger == false, use the following inputs: peak_xls_file_staged: narrow_peak_file_staged: broad_peak_file_staged: gapped_peak_file_staged: peak_summits_file_staged: moder_r_file_staged: treat_pileup_bdg_file_staged: control_lambda_bdg_file_staged:

samtools_rmdup
tools/samtools-rmdup.cwl (CommandLineTool)

This tool is used to remove duplicates from input coordinate sorted BAM file Input Trigger (default: true) allows to skip all calculation and return all input files unchanged. To set files to be returned in case of Trigger == false, use the following inputs: input_file

macs_island_count
tools/macs2-island-count.cwl (CommandLineTool)

Tool is used to return an estimated fragment size and islands count from xls file generated by MACS2 callpeak

fastx_quality_stats
tools/fastx-quality-stats.cwl (CommandLineTool)

Tool is used to calculate statistics on the base of FASTQ file quality scores

samtools_sort_index
tools/samtools-sort-index.cwl (CommandLineTool)

This tool is used to sort and index input BAM/SAM file by means of samtools sort/index Input Trigger (default: true) allows to skip all calculation and return all input files unchanged. To set files to be returned in case of Trigger == false, use the following inputs: sort_input

macs2_callpeak_forced
tools/macs2-callpeak.cwl (CommandLineTool)

Tool is used to perform peak calling using MACS2. Input Trigger (default: true) allows to skip all calculation and return all input files unchanged. To set files to be returned in case of Trigger == false, use the following inputs: peak_xls_file_staged: narrow_peak_file_staged: broad_peak_file_staged: gapped_peak_file_staged: peak_summits_file_staged: moder_r_file_staged: treat_pileup_bdg_file_staged: control_lambda_bdg_file_staged:

samtools_sort_index_after_rmdup
tools/samtools-sort-index.cwl (CommandLineTool)

This tool is used to sort and index input BAM/SAM file by means of samtools sort/index Input Trigger (default: true) allows to skip all calculation and return all input files unchanged. To set files to be returned in case of Trigger == false, use the following inputs: sort_input

Outputs

ID Type Label Doc
bigwig File [bigWig] BigWig file

Generated BigWig file
macs_log File (Optional) [Textual format] MACS2 log

MACS2 output log
bowtie_log File [Textual format] BOWTIE alignment log

BOWTIE generated alignment log
bambai_pair File [BAM] Coordinate sorted BAM alignment file (+index BAI)

Coordinate sorted BAM file and BAI index file
get_stat_log File (Optional) [Textual format] Bowtie & Samtools Rmdup combined log

Processed and combined Bowtie aligner and Samtools rmdup log
macs_moder_r File (Optional) [Textual format] MACS2 generated R script

R script to produce a PDF image about the model based on your data
fastx_statistics File [Textual format] FASTQ statistics

fastx_quality_stats generated FASTQ file quality statistics file
macs_broad_peaks File (Optional) [ENCODE broad peak format] Broad peaks

Contains the peak locations together with peak summit, pvalue and qvalue
macs_gapped_peak File (Optional) [bed12] Gapped peak

Contains both the broad region and narrow peaks
macs_called_peaks File (Optional) [xls] Called peaks

XLS file to include information about called peaks
macs_narrow_peaks File (Optional) [ENCODE narrow peak format] Narrow peaks

Contains the peak locations together with peak summit, pvalue and qvalue
macs_peak_summits File (Optional) [BED] Peak summits

Contains the peak summits locations for every peaks
samtools_rmdup_log File [Textual format] Remove duplicates log

Samtools rmdup generated log
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