Workflow: biowardrobe_chipseq_se.4.cwl
Fetched 2023-01-11 04:19:12 GMT
Verified with cwltool version 3.1.20221201130942
{'extract_fastq': 'http://218.77.58.141:9619','extract_fastq2': 'http://218.77.58.141:9619','extract_fastq3': 'http://121.46.19.86:9619','extract_fastq4': 'http://121.46.19.86:9619', 'fastx_quality_stats': 'http://218.77.58.141:9619','fastx_quality_stats2': 'http://218.77.58.141:9619','fastx_quality_stats3': 'http://121.46.19.86:9619','fastx_quality_stats4': 'http://121.46.19.86:9619','bowtie_aligner': 'http://218.77.58.141:9619','bowtie_aligner2': 'http://218.77.58.141:9619', 'bowtie_aligner3': 'http://121.46.19.86:9619', 'bowtie_aligner4': 'http://121.46.19.86:9619', 'samtools_sort_index': 'http://218.77.58.141:9619','samtools_sort_index2': 'http://218.77.58.141:9619','samtools_sort_index3': 'http://121.46.19.86:9619','samtools_sort_index4': 'http://121.46.19.86:9619', 'samtools_rmdup': 'http://218.77.58.141:9619', 'samtools_rmdup2': 'http://218.77.58.141:9619', 'samtools_rmdup3': 'http://121.46.19.86:9619', 'samtools_rmdup4': 'http://121.46.19.86:9619', 'samtools_sort_index_after_rmdup': 'http://218.77.58.141:9619', 'samtools_sort_index_after_rmdup2': 'http://218.77.58.141:9619', 'samtools_sort_index_after_rmdup3': 'http://121.46.19.86:9619', 'samtools_sort_index_after_rmdup4': 'http://121.46.19.86:9619', 'macs2_callpeak': 'http://218.77.58.141:9619', 'macs2_callpeak2': 'http://218.77.58.141:9619','macs2_callpeak3': 'http://121.46.19.86:9619','macs2_callpeak4': 'http://121.46.19.86:9619', 'get_stat': 'http://218.77.58.141:9619', 'get_stat2': 'http://218.77.58.141:9619', 'get_stat3': 'http://121.46.19.86:9619', 'get_stat4': 'http://121.46.19.86:9619', 'island_intersect': 'http://218.77.58.141:9619', 'island_intersect2': 'http://218.77.58.141:9619', 'island_intersect3': 'http://121.46.19.86:9619', 'island_intersect4': 'http://121.46.19.86:9619', 'average_tag_density': 'http://218.77.58.141:9619', 'average_tag_density2': 'http://218.77.58.141:9619', 'average_tag_density3': 'http://121.46.19.86:9619', 'average_tag_density4': 'http://121.46.19.86:9619' }
- Selected
- |
- 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 |
| 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 |
| fastq_file1 | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format, received after single end sequencing |
| fastq_file2 | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format, received after single end sequencing |
| fastq_file3 | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format, received after single end sequencing |
| fastq_file4 | File [FASTQ] | FASTQ input file |
Reads data in a FASTQ format, received after single end sequencing |
| 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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| get_stat2 |
tools/python-get-stat-chipseq.cwl
(CommandLineTool)
|
||
| get_stat3 |
tools/python-get-stat-chipseq.cwl
(CommandLineTool)
|
||
| get_stat4 |
tools/python-get-stat-chipseq.cwl
(CommandLineTool)
|
||
| extract_fastq |
tools/extract-fastq.cwl
(CommandLineTool)
|
||
| bowtie_aligner |
tools/bowtie-alignreads.cwl
(CommandLineTool)
|
||
| extract_fastq2 |
tools/extract-fastq.cwl
(CommandLineTool)
|
||
| extract_fastq3 |
tools/extract-fastq.cwl
(CommandLineTool)
|
||
| extract_fastq4 |
tools/extract-fastq.cwl
(CommandLineTool)
|
||
| macs2_callpeak |
tools/macs2-callpeak-biowardrobe-only.cwl
(CommandLineTool)
|
||
| samtools_rmdup |
tools/samtools-rmdup.cwl
(CommandLineTool)
|
||
| bowtie_aligner2 |
tools/bowtie-alignreads.cwl
(CommandLineTool)
|
||
| bowtie_aligner3 |
tools/bowtie-alignreads.cwl
(CommandLineTool)
|
||
| bowtie_aligner4 |
tools/bowtie-alignreads.cwl
(CommandLineTool)
|
||
| macs2_callpeak2 |
tools/macs2-callpeak-biowardrobe-only.cwl
(CommandLineTool)
|
||
| macs2_callpeak3 |
tools/macs2-callpeak-biowardrobe-only.cwl
(CommandLineTool)
|
||
| macs2_callpeak4 |
tools/macs2-callpeak-biowardrobe-only.cwl
(CommandLineTool)
|
||
| samtools_rmdup2 |
tools/samtools-rmdup.cwl
(CommandLineTool)
|
||
| samtools_rmdup3 |
tools/samtools-rmdup.cwl
(CommandLineTool)
|
||
| samtools_rmdup4 |
tools/samtools-rmdup.cwl
(CommandLineTool)
|
||
| island_intersect |
tools/iaintersect.cwl
(CommandLineTool)
|
||
| island_intersect2 |
tools/iaintersect.cwl
(CommandLineTool)
|
||
| island_intersect3 |
tools/iaintersect.cwl
(CommandLineTool)
|
||
| island_intersect4 |
tools/iaintersect.cwl
(CommandLineTool)
|
||
| average_tag_density |
tools/atdp.cwl
(CommandLineTool)
|
||
| fastx_quality_stats |
tools/fastx-quality-stats.cwl
(CommandLineTool)
|
||
| samtools_sort_index |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| average_tag_density2 |
tools/atdp.cwl
(CommandLineTool)
|
||
| average_tag_density3 |
tools/atdp.cwl
(CommandLineTool)
|
||
| average_tag_density4 |
tools/atdp.cwl
(CommandLineTool)
|
||
| fastx_quality_stats2 |
tools/fastx-quality-stats.cwl
(CommandLineTool)
|
||
| fastx_quality_stats3 |
tools/fastx-quality-stats.cwl
(CommandLineTool)
|
||
| fastx_quality_stats4 |
tools/fastx-quality-stats.cwl
(CommandLineTool)
|
||
| samtools_sort_index2 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index3 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index4 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index_after_rmdup |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index_after_rmdup2 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index_after_rmdup3 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
||
| samtools_sort_index_after_rmdup4 |
tools/samtools-sort-index.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| atdp_log | File [TSV] | ATDP log |
Average Tag Density generated log |
| atdp_log2 | File [TSV] | ATDP log |
Average Tag Density generated log |
| atdp_log3 | File [TSV] | ATDP log |
Average Tag Density generated log |
| atdp_log4 | 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 |
| macs2_log2 | File (Optional) [Textual format] | MACS2 log |
MACS2 output log |
| macs2_log3 | File (Optional) [Textual format] | MACS2 log |
MACS2 output log |
| macs2_log4 | File (Optional) [Textual format] | MACS2 log |
MACS2 output 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 |
| bowtie_log2 | File [Textual format] | BOWTIE alignment log |
BOWTIE generated alignment log |
| bowtie_log3 | File [Textual format] | BOWTIE alignment log |
BOWTIE generated alignment log |
| bowtie_log4 | File [Textual format] | BOWTIE alignment log |
BOWTIE generated alignment log |
| atdp_result2 | File [TSV] | ATDP results |
Average Tag Density generated results |
| atdp_result3 | File [TSV] | ATDP results |
Average Tag Density generated results |
| atdp_result4 | File [TSV] | ATDP results |
Average Tag Density generated results |
| bambai_pair2 | File [BAM] | Coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file |
| bambai_pair3 | File [BAM] | Coordinate sorted BAM alignment file (+index BAI) |
Coordinate sorted BAM file and BAI index file |
| bambai_pair4 | 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 |
| get_stat_log2 | File (Optional) [Textual format] | Bowtie & Samtools Rmdup combined log |
Processed and combined Bowtie aligner and Samtools rmdup log |
| get_stat_log3 | File (Optional) [Textual format] | Bowtie & Samtools Rmdup combined log |
Processed and combined Bowtie aligner and Samtools rmdup log |
| get_stat_log4 | 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 |
| macs2_moder_r2 | File (Optional) [Textual format] | MACS2 generated R script |
R script to produce a PDF image about the model based on your data |
| macs2_moder_r3 | File (Optional) [Textual format] | MACS2 generated R script |
R script to produce a PDF image about the model based on your data |
| macs2_moder_r4 | 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 |
| iaintersect_log2 | File [TSV] | Island intersect log |
Iaintersect generated log |
| iaintersect_log3 | File [TSV] | Island intersect log |
Iaintersect generated log |
| iaintersect_log4 | File [TSV] | Island intersect log |
Iaintersect generated log |
| fastx_statistics2 | File [Textual format] | FASTQ statistics |
fastx_quality_stats generated FASTQ file quality statistics file |
| fastx_statistics3 | File [Textual format] | FASTQ statistics |
fastx_quality_stats generated FASTQ file quality statistics file |
| fastx_statistics4 | 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_broad_peaks2 | File (Optional) [ENCODE broad peak format] | Broad peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_broad_peaks3 | File (Optional) [ENCODE broad peak format] | Broad peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_broad_peaks4 | File (Optional) [ENCODE broad peak format] | Broad peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_called_peaks | File (Optional) [xls] | Called peaks |
XLS file to include information about called peaks |
| macs2_gapped_peak2 | File (Optional) [bed12] | Gapped peak |
Contains both the broad region and narrow peaks |
| macs2_gapped_peak3 | File (Optional) [bed12] | Gapped peak |
Contains both the broad region and narrow peaks |
| macs2_gapped_peak4 | File (Optional) [bed12] | Gapped peak |
Contains both the broad region and narrow 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 |
| iaintersect_result2 | File [TSV] | Island intersect results |
Iaintersect generated results |
| iaintersect_result3 | File [TSV] | Island intersect results |
Iaintersect generated results |
| iaintersect_result4 | File [TSV] | Island intersect results |
Iaintersect generated results |
| macs2_called_peaks2 | File (Optional) [xls] | Called peaks |
XLS file to include information about called peaks |
| macs2_called_peaks3 | File (Optional) [xls] | Called peaks |
XLS file to include information about called peaks |
| macs2_called_peaks4 | File (Optional) [xls] | Called peaks |
XLS file to include information about called peaks |
| macs2_narrow_peaks2 | File (Optional) [ENCODE narrow peak format] | Narrow peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_narrow_peaks3 | File (Optional) [ENCODE narrow peak format] | Narrow peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_narrow_peaks4 | File (Optional) [ENCODE narrow peak format] | Narrow peaks |
Contains the peak locations together with peak summit, pvalue and qvalue |
| macs2_peak_summits2 | File (Optional) [BED] | Peak summits |
Contains the peak summits locations for every peaks |
| macs2_peak_summits3 | File (Optional) [BED] | Peak summits |
Contains the peak summits locations for every peaks |
| macs2_peak_summits4 | File (Optional) [BED] | Peak summits |
Contains the peak summits locations for every peaks |
https://w3id.org/cwl/view/git/2dde67eadd96ade931efd7d15a8c094f73a76463/biowardrobe_chipseq_se.4.cwl
