CWL Workflow: 03-map-se.cwl

Workflow: 03-map-se.cwl

Fetched 2024-11-24 13:09:19 GMT

Verified with cwltool version 3.1.20221201130942

ATAC-seq 03 mapping - reads: SE

Selected
|
Default Values
Nested Workflows
Tools
Inputs/Outputs

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Doc
nthreads	Integer
picard_jar_path	String	Picard Java jar file
picard_java_opts	String (Optional)	JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\")
genome_sizes_file	File	Genome sizes tab-delimited file (used in samtools)
input_fastq_files	File[]	Input fastq files
genome_ref_first_index_file	File	Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder.

Steps

ID	Runs	Doc
sam2bam	../map/samtools2bam.cwl (CommandLineTool)
bowtie-se	../map/bowtie-se.cwl (CommandLineTool)
sort_bams	../map/samtools-sort.cwl (CommandLineTool)
index_bams	../map/samtools-index.cwl (CommandLineTool)
bam_idxstats	../map/samtools-idxstats.cwl (CommandLineTool)
preseq-c-curve	../map/preseq-c_curve.cwl (CommandLineTool)	Usage: c_curve [OPTIONS] <sorted-bed-file> Options: -o, -output yield output file (default: stdout) -s, -step step size in extrapolations (default: 1e+06) -v, -verbose print more information -P, -pe input is paired end read file -H, -hist input is a text file containing the observed histogram -V, -vals input is a text file containing only the observed counts -B, -bam input is in BAM format -l, -seg_len maximum segment length when merging paired end bam reads (default: 5000) Help options: -?, -help print this help message -about print about message
filter-unmapped	../map/samtools-filter-unmapped.cwl (CommandLineTool)
filtered2sorted	../map/samtools-sort.cwl (CommandLineTool)
mark_duplicates	../map/picard-MarkDuplicates.cwl (CommandLineTool)
sort_dedup_bams	../map/samtools-sort.cwl (CommandLineTool)
index_dedup_bams	../map/samtools-index.cwl (CommandLineTool)
remove_duplicates	../map/samtools-view.cwl (CommandLineTool)
extract_basename_1	../utils/basename.cwl (ExpressionTool)
index_filtered_bam	../map/samtools-index.cwl (CommandLineTool)
mapped_reads_count	../map/bowtie-log-read-count.cwl (CommandLineTool)	Get number of processed reads from Bowtie log.
percent_uniq_reads	../map/preseq-percent-uniq-reads.cwl (CommandLineTool)	Get number of processed reads from Bowtie log.
sort_dups_marked_bams	../map/samtools-sort.cwl (CommandLineTool)
index_dups_marked_bams	../map/samtools-index.cwl (CommandLineTool)
execute_pcr_bottleneck_coef	../map/pcr-bottleneck-coef.cwl (Workflow)	ChIP-seq - map - PCR Bottleneck Coefficients
mapped_filtered_reads_count	../peak_calling/samtools-extract-number-mapped-reads.cwl (CommandLineTool)	Extract mapped reads from BAM file using Samtools flagstat command
percent_mitochondrial_reads	../utils/idxstats-percentage-of-reads-in-chrom.cwl (ExpressionTool)

Outputs

ID	Type	Doc
output_pbc_files	File[]	PCR Bottleneck Coeficient files.
output_bowtie_log	File[]	Bowtie log file.
output_read_count_mapped	File[]	Read counts of the mapped BAM files
output_preseq_c_curve_files	File[]	Preseq c_curve output files.
output_percentage_uniq_reads	File[]	Percentage of uniq reads from preseq c_curve output
output_read_count_mapped_filtered	File[]	Read counts of the mapped and filtered BAM files
output_data_sorted_dedup_bam_files	File[]	BAM files without duplicate reads.
output_percent_mitochondrial_reads	File[]	Percentage of mitochondrial reads.
output_picard_mark_duplicates_files	File[]	Picard MarkDuplicates metrics files.
output_data_sorted_dups_marked_bam_files	File[]	BAM files with marked duplicate reads.

Permalink: https://w3id.org/cwl/view/git/1a0dd34d59ec983d1f7ad77bff35da2f016e3134/v1.0/ATAC-seq_pipeline/03-map-se.cwl