Workflow: wf_get_peaks_scatter_se.cwl

Fetched 2023-01-04 10:51:51 GMT

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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Inputs

ID Type Title Doc
dataset String
samples fd2e2336789b37371dd7ce7e9c42efc1[]
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_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 ab66e7b34533a3a2fc8a9cd4f1e7efcd[]
output_ip_b1_trimx2_fastq 2f8aba9eeb7be5a75569064fc1077675[]
output_ip_b1_trimx1_metrics File[]
output_ip_b1_trimx2_metrics File[]
output_blacklist_removed_bed File[]
output_input_b1_trimx1_fastq dfecc3df7480df2feba915143434cc49[]
output_input_b1_trimx2_fastq 4ae41b62e3eb62d0298fab00d76e24ed[]
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/6b533898c395e9e5b9d0acc1587d0c68bc56abe0/cwl/wf_get_peaks_scatter_se.cwl