Workflow: wf_get_peaks_scatter_chimeric_se.cwl
Fetched 2023-01-09 17:28:48 GMT
Verified with cwltool version 3.1.20221201130942
The \"main\" workflow. Takes fastq files generated using the seCLIP protocol (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991800/) and outputs candidate RBP binding regions (peaks). runs: wf_get_peaks_se.cwl through scatter across multiple samples.
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- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
BSD 3-clause "New" or "Revised" License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dataset | String | ||
| samples | e587077f9559f9923a8c7f50078d716b[] | ||
| species | String | ||
| chrom_sizes | File | ||
| blacklist_file | File | ||
| speciesGenomeDir | Directory | ||
| repeatElementGenomeDir | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step_get_peaks |
wf_get_peaks_chimeric_se.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_bigbed | File[] | ||
| output_fixed_bed | File[] | ||
| output_ip_neg_bw | File[] | ||
| output_ip_pos_bw | File[] | ||
| output_entropynum | File[] | ||
| output_narrowpeak | File[] | ||
| output_clipper_bed | File[] | ||
| output_input_neg_bw | File[] | ||
| output_input_pos_bw | File[] | ||
| output_compressed_peaks | File[] | ||
| output_inputnormed_peaks | File[] | ||
| output_ip_b1_trimx1_fastq | 35b3003573ca440bb0b91f1bad966f91[] | ||
| output_ip_b1_trimx2_fastq | 7b59f85ac07b4e8ed4cdbd0428c4820a[] | ||
| output_ip_b1_trimx1_metrics | File[] | ||
| output_ip_b1_trimx2_metrics | File[] | ||
| output_blacklist_removed_bed | File[] | ||
| output_input_b1_trimx1_fastq | a0c6089997730f3d89382f079a7229d8[] | ||
| output_input_b1_trimx2_fastq | e657dfb77d9c441854e7e1f56ed1d5a1[] | ||
| output_ip_b1_mapgenome_stats | File[] | ||
| output_ip_b1_demuxed_fastq_r1 | File[] | ||
| output_ip_b1_maprepeats_stats | File[] | ||
| output_ip_b1_rmdup_sorted_bam | File[] | ||
| output_input_b1_trimx1_metrics | File[] | ||
| output_input_b1_trimx2_metrics | File[] | ||
| output_input_b1_mapgenome_stats | File[] | ||
| output_input_b1_demuxed_fastq_r1 | File[] | ||
| output_input_b1_maprepeats_stats | File[] | ||
| output_input_b1_rmdup_sorted_bam | File[] | ||
| output_ip_b1_trimx1_fastqc_stats | File[] | ||
| output_ip_b1_trimx2_fastqc_stats | File[] | ||
| output_ip_b1_pre_rmdup_sorted_bam | File[] | ||
| output_ip_b1_trimx1_fastqc_report | File[] | ||
| output_ip_b1_trimx2_fastqc_report | File[] | ||
| output_ip_b1_sorted_unmapped_fastq | File[] | ||
| output_input_b1_trimx1_fastqc_stats | File[] | ||
| output_input_b1_trimx2_fastqc_stats | File[] | ||
| output_input_b1_pre_rmdup_sorted_bam | File[] | ||
| output_input_b1_trimx1_fastqc_report | File[] | ||
| output_input_b1_trimx2_fastqc_report | File[] | ||
| output_ip_b1_mapgenome_star_settings | File[] | ||
| output_input_b1_sorted_unmapped_fastq | File[] | ||
| output_ip_b1_maprepeats_star_settings | File[] | ||
| output_ip_b1_barcodecollapsese_metrics | File[] | ||
| output_input_b1_mapgenome_star_settings | File[] | ||
| output_ip_b1_mapgenome_mapped_to_genome | File[] | ||
| output_input_b1_maprepeats_star_settings | File[] | ||
| output_ip_b1_maprepeats_mapped_to_genome | File[] | ||
| output_input_b1_barcodecollapsese_metrics | File[] | ||
| output_input_b1_mapgenome_mapped_to_genome | File[] | ||
| output_input_b1_maprepeats_mapped_to_genome | File[] |
Permalink:
https://w3id.org/cwl/view/git/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_get_peaks_scatter_chimeric_se.cwl
