Workflow: wf_get_peaks_scatter_pe.cwl
Fetched 2023-01-03 19:42:57 GMT
Verified with cwltool version 3.1.20221201130942
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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 | a21e60a88102f44db52f869b6f3bf36c[] | ||
| 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 | 569741ed975c180588fe2d7ca28ec127[] | ||
| output_ip_b1_trimx2_fastq | c903b436faaf872bfb25d4b0fe17ca07[] | ||
| output_ip_b2_trimx1_fastq | d183f7c5a2c2b726dd274cd19aca0a46[] | ||
| output_ip_b2_trimx2_fastq | d211f263372c7d6920f2ad094b8b9e81[] | ||
| 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 | 9e0fe89c87dbdcde5de7fbd06d229541[] | ||
| output_input_b1_trimx2_fastq | 78884058586e259bfd18fef9c8d1f7b8[] | ||
| 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 | 636871f370868270ee7768c96f230657[] | ||
| output_ip_b2_barcodecollapsepe_bam | File[] | ||
| output_ip_b2_sorted_unmapped_fastq | 4b5fdbe65700b363b7cb9f025b0fab8b[] | ||
| 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 | 18070b21bfc57d41a76122a61513290b[] | ||
| 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/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_get_peaks_scatter_pe.cwl
