Workflow: wf_clipseqcore_pe_1barcode.cwl

Fetched 2020-08-14 16:27:40 GMT
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ID Type Title Doc
chrom_sizes File
speciesGenomeDir Directory
repeatElementGenomeDir Directory
barcodesfasta File
species String
randomer_length String
dataset String


ID Runs Label Doc
makebigwigfiles_PE.cwl (CommandLineTool)

Creates strand-specific bigwig files from a BAM file. See original script here: Usage: makebigwigfiles --bam BAM --genome GENOME --dont_flip --bw_pos --bw_neg

file2string.cwl (ExpressionTool)

Returns string expression based on file contents.

file2string.cwl (ExpressionTool)

Returns string expression based on file contents.

samtools-viewr2.cwl (CommandLineTool)

samtools-view.cwl is developed for CWL consortium Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -T FILE reference sequence FASTA FILE [null] -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all bits set in INT set in FLAG [0] -F INT only include reads with none of the bits set in INT set in FLAG [0] -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] -@ INT number of BAM compression threads [0]


This workflow takes in appropriate trimming params and demultiplexed reads, and performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment


ID Type Label Doc
b1_demuxed_fastq_r1 File Barcode1 read1 demultiplexed fastq
b1_demuxed_fastq_r2 File
b1_output_barcodecollapsepe_bam File
b1_sorted_unmapped_fastq File[]
b1_trimx1_metrics File
b1_maprepeats_mapped_to_genome File
b1_trimx1_fastq File[]
b1_trimx2_fastqc_stats_R1 File
b1_mapgenome_stats File
b1_trimx2_fastqc_stats_R2 File
output_neg_bw File
b1_trimx2_metrics File
b1_output_sorted_bam File
b1_mapgenome_mapped_to_genome File
b1_maprepeats_stats File
b1_trimx2_fastqc_report_R1 File
b1_trimx2_fastqc_report_R2 File
b1_mapgenome_star_settings File
output_pos_bw File
b1_trimx2_fastq File[]
b1_output_prermdup_sorted_bam File
output_r2_bam File
b1_maprepeats_star_settings File
b1_trimx1_fastqc_report_R2 File
b1_output_barcodecollapsepe_metrics File
b1_trimx1_fastqc_stats_R1 File
b1_trimx1_fastqc_stats_R2 File
b1_trimx1_fastqc_report_R1 File