Workflow: biowardrobe_chipseq_se.cwl
Fetched 2024-11-23 04:50:13 GMT
Verified with cwltool version 3.1.20221201130942
The 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.
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| threads | Integer (Optional) | Number of threads |
Number of threads for those steps that support multithreading |
| broad_peak | Boolean | Callpeak broad |
Set to call broad peak for MACS2 |
| fastq_file | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format, received after single end sequencing |
| clip_3p_end | Integer (Optional) | Clip from 3p end |
Number of bases to clip from the 3p end |
| clip_5p_end | Integer (Optional) | 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 |
| indices_folder | Directory | BOWTIE indices folder |
Path to BOWTIE generated indices folder |
| annotation_file | File [TSV] | Annotation file |
Tab-separated input annotation file |
| exp_fragment_size | Integer (Optional) | Expected fragment size |
Expected fragment size for MACS2 |
| remove_duplicates | Boolean (Optional) | Remove duplicates |
Calls samtools rmdup to remove duplicates from sortesd BAM file |
| force_fragment_size | Boolean (Optional) | Force fragment size |
Force MACS2 to use exp_fragment_size |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| get_stat |
tools/python-get-stat-chipseq.cwl
(CommandLineTool)
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| bam_to_bigwig |
subworkflows/bam-bedgraph-bigwig.cwl
(Workflow)
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| extract_fastq |
tools/extract-fastq.cwl
(CommandLineTool)
|
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| bowtie_aligner |
tools/bowtie-alignreads.cwl
(CommandLineTool)
|
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| macs2_callpeak |
tools/macs2-callpeak-biowardrobe-only.cwl
(CommandLineTool)
|
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| samtools_rmdup |
tools/samtools-rmdup.cwl
(CommandLineTool)
|
||
| island_intersect |
tools/iaintersect.cwl
(CommandLineTool)
|
||
| average_tag_density |
tools/atdp.cwl
(CommandLineTool)
|
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| fastx_quality_stats |
tools/fastx-quality-stats.cwl
(CommandLineTool)
|
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| samtools_sort_index |
tools/samtools-sort-index.cwl
(CommandLineTool)
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| samtools_sort_index_after_rmdup |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bigwig | File [bigWig] | BigWig file |
Generated BigWig file |
| atdp_log | File [TSV] | ATDP log |
Average Tag Density generated log |
| macs2_log | File (Optional) [Textual format] | MACS2 log |
MACS2 output log |
| bowtie_log | File [Textual format] | BOWTIE alignment log |
BOWTIE generated alignment log |
| atdp_result | File [TSV] | ATDP results |
Average Tag Density generated results |
| 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 |
| macs2_moder_r | File (Optional) [Textual format] | MACS2 generated R script |
R script to produce a PDF image about the model based on your data |
| iaintersect_log | File [TSV] | Island intersect log |
Iaintersect generated log |
| fastx_statistics | File [Textual format] | FASTQ statistics |
fastx_quality_stats generated FASTQ file quality statistics file |
| macs2_broad_peaks | File (Optional) [ENCODE broad peak format] | Broad peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_gapped_peak | File (Optional) [bed12] | Gapped peak |
Contains both the broad region and narrow peaks |
| iaintersect_result | File [TSV] | Island intersect results |
Iaintersect generated results |
| macs2_called_peaks | File (Optional) [xls] | Called peaks |
XLS file to include information about called peaks |
| macs2_narrow_peaks | File (Optional) [ENCODE narrow peak format] | Narrow peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_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 |
| macs2_fragment_stat | File (Optional) [Textual format] | FRAGMENT, FRAGMENTE, ISLANDS |
fragment, calculated fragment, islands count from MACS2 results |
https://w3id.org/cwl/view/git/f28d47bd0911e5e7210c4dc83f75653a1e0297c9/biowardrobe_chipseq_se.cwl
