Workflow: wf_clipseqcore_pe_2barcodes.cwl
Workflow for handling reads containing two barcodes. Returns the bam file containing read2 only. Notes: runs the following steps: - demultiplex - trimfirst_file2string - trimagain_file2string - b1_trim_and_map - view_r2 - index_r2_bam - make_bigwigs
- Selected
- |
- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
---|---|---|---|
read | |||
dataset | String | ||
chrom_sizes | File | ||
barcodesfasta | File | ||
randomer_length | String | ||
speciesGenomeDir | Directory | ||
repeatElementGenomeDir | Directory |
Steps
ID | Runs | Label | Doc |
---|---|---|---|
merge |
samtools-merge.cwl
(CommandLineTool)
|
samtools-merge.cwl takes in a list of input_bam_files and
returns a merged BAM file. |
|
view_r2 |
samtools-viewr2.cwl
(CommandLineTool)
|
samtools-view.cwl is developed for CWL consortium
Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...] |
|
demultiplex |
wf_demultiplex_pe.cwl
(Workflow)
|
||
index_r2_bam |
samtools-index.cwl
(CommandLineTool)
|
samtools-index.cwl is developed for CWL consortium |
|
make_bigwigs |
makebigwigfiles_PE.cwl
(CommandLineTool)
|
Creates strand-specific bigwig files from a BAM file. See original script here: https://github.com/YeoLab/gscripts/blob/master/gscripts/general/make_bigwig_files_pe.py Usage: makebigwigfiles --bam BAM --genome GENOME --dont_flip --bw_pos --bw_neg |
|
b1_trim_and_map |
wf_trim_and_map_pe.cwl
(Workflow)
|
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 |
|
b2_trim_and_map |
wf_trim_and_map_pe.cwl
(Workflow)
|
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 |
|
trimagain_file2string |
file2string.cwl
(ExpressionTool)
|
Returns string expression based on file contents. |
|
trimfirst_file2string |
file2string.cwl
(ExpressionTool)
|
Returns string expression based on file contents. |
Outputs
ID | Type | Label | Doc |
---|---|---|---|
output_neg_bw | File | ||
output_pos_bw | File | ||
output_r2_bam | File | ||
b1_trimx1_fastq | File[] | ||
b1_trimx2_fastq | File[] | ||
b2_trimx1_fastq | File[] | ||
b2_trimx2_fastq | File[] | ||
b1_trimx1_metrics | File | ||
b1_trimx2_metrics | File | ||
b2_trimx1_metrics | File | ||
b2_trimx2_metrics | File | ||
b1_mapgenome_stats | File | ||
b2_mapgenome_stats | File | ||
b1_demuxed_fastq_r1 | File | ||
b1_demuxed_fastq_r2 | File | ||
b1_maprepeats_stats | File | ||
b2_demuxed_fastq_r1 | File | ||
b2_demuxed_fastq_r2 | File | ||
b2_maprepeats_stats | File | ||
b1_output_sorted_bam | File | ||
b2_output_sorted_bam | File | ||
b1_sorted_unmapped_fastq | File[] | ||
b2_sorted_unmapped_fastq | File[] | ||
b1_trimx1_fastqc_stats_R1 | File | ||
b1_trimx1_fastqc_stats_R2 | File | ||
b1_trimx2_fastqc_stats_R1 | File | ||
b1_trimx2_fastqc_stats_R2 | File | ||
b2_trimx1_fastqc_stats_R1 | File | ||
b2_trimx1_fastqc_stats_R2 | File | ||
b2_trimx2_fastqc_stats_R1 | File | ||
b2_trimx2_fastqc_stats_R2 | File | ||
b1_mapgenome_star_settings | File | ||
b1_trimx1_fastqc_report_R1 | File | ||
b1_trimx1_fastqc_report_R2 | File | ||
b1_trimx2_fastqc_report_R1 | File | ||
b1_trimx2_fastqc_report_R2 | File | ||
b2_mapgenome_star_settings | File | ||
b2_trimx1_fastqc_report_R1 | File | ||
b2_trimx1_fastqc_report_R2 | File | ||
b2_trimx2_fastqc_report_R1 | File | ||
b2_trimx2_fastqc_report_R2 | File | ||
b1_maprepeats_star_settings | File | ||
b2_maprepeats_star_settings | File | ||
b1_mapgenome_mapped_to_genome | File | ||
b1_output_prermdup_sorted_bam | File | ||
b2_mapgenome_mapped_to_genome | File | ||
b2_output_prermdup_sorted_bam | File | ||
b1_maprepeats_mapped_to_genome | File | ||
b2_maprepeats_mapped_to_genome | File | ||
b1_output_barcodecollapsepe_bam | File | ||
b2_output_barcodecollapsepe_bam | File | ||
b1_output_barcodecollapsepe_metrics | File | ||
b2_output_barcodecollapsepe_metrics | File |
https://w3id.org/cwl/view/git/49a9bcda10de8f55fab2481f424eb9cdf2e5b256/cwl/wf_clipseqcore_pe_2barcodes.cwl