Workflow: wf_get_peaks_scatter_se.cwl
Fetched 2024-05-01 14:55:21 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.
- Selected
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- Default Values
- Nested Workflows
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/YeoLab/eclip/master/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dataset | String | ||
| samples | 3636d807fac80cb44db3ebb79aec8d1d[] | ||
| species | String | ||
| chrom_sizes | File | ||
| blacklist_file | File | ||
| speciesGenomeDir | Directory | ||
| repeatElementGenomeDir | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step_get_peaks |
wf_get_peaks_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 | adc50eab0b840c5d87263a012064ccb7[] | ||
| output_ip_b1_trimx2_fastq | ad3490af5964c7ed56404cb6de451975[] | ||
| output_ip_b1_trimx1_metrics | File[] | ||
| output_ip_b1_trimx2_metrics | File[] | ||
| output_blacklist_removed_bed | File[] | ||
| output_input_b1_trimx1_fastq | 3162df5322bc5d57a2b1851ec3f002b7[] | ||
| output_input_b1_trimx2_fastq | d9f70e3eedab3a3a95f9d923b2450561[] | ||
| 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/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_get_peaks_scatter_se.cwl
