Workflow: wf_get_peaks_scatter_pe.cwl
Fetched 2023-05-27 22:02:27 GMT
Verified with cwltool version 3.1.20230201224320
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This workflow is Open Source and may be reused according to the terms of:
https://raw.githubusercontent.com/YeoLab/eclip/c0fffc4979a92371dc0667a03e3d957bf7f77600/LICENSE
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| dataset | String | ||
| samples | a2dd584fe30ec7db8ea8450162314b90[] | ||
| species | String | ||
| chrom_sizes | File | ||
| barcodesfasta | File | ||
| randomer_length | String | ||
| speciesGenomeDir | Directory | ||
| repeatElementGenomeDir | Directory |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| step_get_peaks |
wf_get_peaks_pe.cwl
(Workflow)
|
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| output_input_bam | File[] | ||
| output_ip_neg_bw | File[] | ||
| output_ip_pos_bw | File[] | ||
| output_entropynum | File[] | ||
| output_clipper_bed | File[] | ||
| output_input_neg_bw | File[] | ||
| output_input_pos_bw | File[] | ||
| output_ip_merged_bam | File[] | ||
| output_compressed_peaks | File[] | ||
| output_inputnormed_peaks | File[] | ||
| output_ip_b1_trimx1_fastq | f3297237668358e15b17f66c5eebd003[] | ||
| output_ip_b1_trimx2_fastq | ffae42b135c2c0efdc29dab3939985d3[] | ||
| output_ip_b2_trimx1_fastq | 8de129415925e54b885c314ccf1d385c[] | ||
| output_ip_b2_trimx2_fastq | e6853298e25424f74945af3d047e5616[] | ||
| output_ip_b1_trimx1_metrics | File[] | ||
| output_ip_b1_trimx2_metrics | File[] | ||
| output_ip_b2_trimx1_metrics | File[] | ||
| output_ip_b2_trimx2_metrics | File[] | ||
| output_input_b1_trimx1_fastq | c83c447e9ef04e2ca1b065a7631a6585[] | ||
| output_input_b1_trimx2_fastq | a27b3a01552b239b7a0934dfcdf84b43[] | ||
| output_ip_b1_mapgenome_stats | File[] | ||
| output_ip_b2_mapgenome_stats | File[] | ||
| output_ip_b1_demuxed_fastq_r1 | File[] | ||
| output_ip_b1_demuxed_fastq_r2 | File[] | ||
| output_ip_b1_maprepeats_stats | File[] | ||
| output_ip_b2_demuxed_fastq_r1 | File[] | ||
| output_ip_b2_demuxed_fastq_r2 | File[] | ||
| output_ip_b2_maprepeats_stats | File[] | ||
| output_input_b1_trimx1_metrics | File[] | ||
| output_input_b1_trimx2_metrics | File[] | ||
| output_ip_b1_output_sorted_bam | File[] | ||
| output_ip_b2_output_sorted_bam | File[] | ||
| output_input_b1_mapgenome_stats | File[] | ||
| output_input_b1_demuxed_fastq_r1 | File[] | ||
| output_input_b1_demuxed_fastq_r2 | File[] | ||
| output_input_b1_maprepeats_stats | File[] | ||
| output_ip_b1_prermdup_sorted_bam | File[] | ||
| output_ip_b2_prermdup_sorted_bam | File[] | ||
| output_input_b1_output_sorted_bam | File[] | ||
| output_ip_b1_barcodecollapsepe_bam | File[] | ||
| output_ip_b1_sorted_unmapped_fastq | 16d85a34114554056b3233e00d3c449b[] | ||
| output_ip_b2_barcodecollapsepe_bam | File[] | ||
| output_ip_b2_sorted_unmapped_fastq | 7f6e3096ebe832218b745f5028f15a72[] | ||
| output_input_b1_prermdup_sorted_bam | File[] | ||
| output_ip_b1_trimx1_fastqc_stats_R1 | File[] | ||
| output_ip_b1_trimx1_fastqc_stats_R2 | File[] | ||
| output_ip_b1_trimx2_fastqc_stats_R1 | File[] | ||
| output_ip_b1_trimx2_fastqc_stats_R2 | File[] | ||
| output_ip_b2_trimx1_fastqc_stats_R1 | File[] | ||
| output_ip_b2_trimx1_fastqc_stats_R2 | File[] | ||
| output_ip_b2_trimx2_fastqc_stats_R1 | File[] | ||
| output_ip_b2_trimx2_fastqc_stats_R2 | File[] | ||
| output_ip_b1_mapgenome_star_settings | File[] | ||
| output_ip_b1_trimx1_fastqc_report_R1 | File[] | ||
| output_ip_b1_trimx1_fastqc_report_R2 | File[] | ||
| output_ip_b1_trimx2_fastqc_report_R1 | File[] | ||
| output_ip_b1_trimx2_fastqc_report_R2 | File[] | ||
| output_ip_b2_mapgenome_star_settings | File[] | ||
| output_ip_b2_trimx1_fastqc_report_R1 | File[] | ||
| output_ip_b2_trimx1_fastqc_report_R2 | File[] | ||
| output_ip_b2_trimx2_fastqc_report_R1 | File[] | ||
| output_ip_b2_trimx2_fastqc_report_R2 | File[] | ||
| output_input_b1_barcodecollapsepe_bam | File[] | ||
| output_input_b1_sorted_unmapped_fastq | 8bc2d36510f5ee4c2ba122ef8a7f987f[] | ||
| output_ip_b1_maprepeats_star_settings | File[] | ||
| output_ip_b2_maprepeats_star_settings | File[] | ||
| output_input_b1_trimx1_fastqc_stats_R1 | File[] | ||
| output_input_b1_trimx1_fastqc_stats_R2 | File[] | ||
| output_input_b1_trimx2_fastqc_stats_R1 | File[] | ||
| output_input_b1_trimx2_fastqc_stats_R2 | File[] | ||
| output_ip_b1_barcodecollapsepe_metrics | File[] | ||
| output_ip_b2_barcodecollapsepe_metrics | File[] | ||
| output_input_b1_mapgenome_star_settings | File[] | ||
| output_input_b1_trimx1_fastqc_report_R1 | File[] | ||
| output_input_b1_trimx1_fastqc_report_R2 | File[] | ||
| output_input_b1_trimx2_fastqc_report_R1 | File[] | ||
| output_input_b1_trimx2_fastqc_report_R2 | File[] | ||
| output_ip_b1_mapgenome_mapped_to_genome | File[] | ||
| output_ip_b2_mapgenome_mapped_to_genome | File[] | ||
| output_input_b1_maprepeats_star_settings | File[] | ||
| output_ip_b1_maprepeats_mapped_to_genome | File[] | ||
| output_ip_b2_maprepeats_mapped_to_genome | File[] | ||
| output_input_b1_barcodecollapsepe_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_pe.cwl
