Workflow: ATACseq_pipeline.cwl
Fetched 2023-01-13 06:47:05 GMT
Verified with cwltool version 3.1.20221201130942
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Unknown workflow license, check
source repository.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| fastq1 | File[] | ||
| fastq2 | File[] | ||
| adapter1 | String[] | ||
| adapter2 | String[] | ||
| bin_size | Integer | ||
| reference | File | ||
| sample_id | String | ||
| macs2_qvalue | Float | ||
| reference_info | File | ||
| macs2_genome_size | String | ||
| effective_genome_size | Long | ||
| ignoreForNormalization | String[] | ||
| max_mapping_insert_length | Long |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| trim_and_map |
../workflow_modules/trim_and_map.cwl
(Workflow)
|
||
| merge_duprem_filter |
../workflow_modules/merge_duprem_filter.cwl
(Workflow)
|
||
| qc_plot_fingerprint |
../tools/deeptools_plotFingerprint.cwl
(CommandLineTool)
|
||
| converting_bam_to_bedpe |
../tools/bedtools_bamtobed_pe.cwl
(CommandLineTool)
|
||
| qc_phantompeakqualtools |
../tools/phantompeakqualtools.cwl
(CommandLineTool)
|
||
| create_summary_qc_report |
../tools/multiqc_hack.cwl
(CommandLineTool)
|
||
| peak_calling_macs2_broad |
../tools/macs2_callpeak_atac.cwl
(CommandLineTool)
|
||
| name_sorting_filtered_bam |
../tools/samtools_sort_name.cwl
(CommandLineTool)
|
Sort a bam file by read names. |
|
| peak_calling_macs2_narrow |
../tools/macs2_callpeak_atac.cwl
(CommandLineTool)
|
||
| generating_coverage_tracks | |||
| generating_atac_signal_tags |
../tools/generate_atac_signal_tags.cwl
(CommandLineTool)
|
||
| plot_fragment_size_distribution |
../tools/plot_frag_size_distr.cwl
(CommandLineTool)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| bam | File | ||
| bowtie2_log | File[] | ||
| multiqc_zip | File | ||
| multiqc_html | File | ||
| raw_fastqc_zip | d28ef2b2109c1fe00386a6efc009896c[] | ||
| bam_signal_tags | File[] | ||
| raw_fastqc_html | 36a59d50d7c035f7c7d5567f9d98bf1d[] | ||
| trim_galore_log | ed53163bcb7c907558303f6f39079fff[] | ||
| duprem_fastqc_zip | File[] | ||
| qc_crosscorr_plot | File (Optional) | ||
| bigwig_signal_tags | File[] | ||
| duprem_fastqc_html | File[] | ||
| fragment_sizes_tsv | File | ||
| picard_markdup_log | File | ||
| trimmed_fastqc_zip | c7d316ae8774b8a1398dd67ed3632d41[] | ||
| filtering_stats_tsv | File | ||
| frag_size_distr_tsv | File | ||
| frag_size_stats_tsv | File | ||
| trimmed_fastqc_html | 2c1ecaf362e8c8a2a3378c0fbd701a75[] | ||
| frag_size_distr_plot | File | ||
| irreg_mappings_bedpe | File | ||
| qc_crosscorr_summary | File (Optional) | ||
| peaks_bed_macs2_broad | d6390c5956aec4d366e50552807bcf8d[] | ||
| peaks_xls_macs2_broad | File[] | ||
| duprem_flagstat_output | File | ||
| merged_flagstat_output | File | ||
| peaks_bed_macs2_narrow | File[] | ||
| peaks_xls_macs2_narrow | File | ||
| qc_plot_fingerprint_tsv | File (Optional) | ||
| filtered_flagstat_output | File | ||
| qc_plot_fingerprint_plot | File (Optional) | ||
| qc_plot_fingerprint_stderr | File | ||
| qc_phantompeakqualtools_stderr | File (Optional) |
Permalink:
https://w3id.org/cwl/view/git/52515b5c053d3cf157be070efac954043892429f/CWL/workflows/ATACseq_pipeline.cwl
