Workflow: 03-map-se.cwl

Fetched 2023-01-10 02:38:56 GMT

ATAC-seq 03 mapping - reads: SE

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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs genome_sizes_file genome_sizes_file execute_pcr_bottleneck_coef execute_pcr_bottleneck_coef genome_sizes_file->execute_pcr_bottleneck_coef genome_sizes input_fastq_files input_fastq_files bowtie-se bowtie-se input_fastq_files->bowtie-se input_fastq_file extract_basename_1 extract_basename_1 input_fastq_files->extract_basename_1 input_file genome_ref_first_index_file genome_ref_first_index_file genome_ref_first_index_file->bowtie-se genome_ref_first_index_file picard_java_opts picard_java_opts mark_duplicates mark_duplicates picard_java_opts->mark_duplicates java_opts nthreads nthreads nthreads->bowtie-se nthreads sort_dedup_bams sort_dedup_bams nthreads->sort_dedup_bams nthreads filtered2sorted filtered2sorted nthreads->filtered2sorted nthreads sort_dups_marked_bams sort_dups_marked_bams nthreads->sort_dups_marked_bams nthreads sam2bam sam2bam nthreads->sam2bam nthreads sort_bams sort_bams nthreads->sort_bams nthreads picard_jar_path picard_jar_path picard_jar_path->mark_duplicates picard_jar_path output_read_count_mapped_filtered output_read_count_mapped_filtered output_read_count_mapped output_read_count_mapped output_data_sorted_dups_marked_bam_files output_data_sorted_dups_marked_bam_files output_percent_mitochondrial_reads output_percent_mitochondrial_reads output_preseq_c_curve_files output_preseq_c_curve_files output_percentage_uniq_reads output_percentage_uniq_reads output_bowtie_log output_bowtie_log output_data_sorted_dedup_bam_files output_data_sorted_dedup_bam_files output_pbc_files output_pbc_files output_picard_mark_duplicates_files output_picard_mark_duplicates_files bowtie-se->output_bowtie_log mapped_reads_count mapped_reads_count bowtie-se->mapped_reads_count bowtie_log bowtie-se->sam2bam input_file index_dedup_bams index_dedup_bams index_dedup_bams->output_data_sorted_dedup_bam_files percent_mitochondrial_reads percent_mitochondrial_reads percent_mitochondrial_reads->output_percent_mitochondrial_reads remove_duplicates remove_duplicates remove_duplicates->sort_dedup_bams input_file execute_pcr_bottleneck_coef->output_pbc_files preseq-c-curve preseq-c-curve preseq-c-curve->output_preseq_c_curve_files percent_uniq_reads percent_uniq_reads preseq-c-curve->percent_uniq_reads preseq_c_curve_outfile mapped_reads_count->output_read_count_mapped index_filtered_bam index_filtered_bam index_filtered_bam->mark_duplicates input_file percent_uniq_reads->output_percentage_uniq_reads index_dups_marked_bams index_dups_marked_bams index_dups_marked_bams->output_data_sorted_dups_marked_bam_files index_dups_marked_bams->remove_duplicates input_file mapped_filtered_reads_count mapped_filtered_reads_count mapped_filtered_reads_count->output_read_count_mapped_filtered sort_dedup_bams->index_dedup_bams input_file sort_dedup_bams->mapped_filtered_reads_count input_bam_file filtered2sorted->execute_pcr_bottleneck_coef input_bam_files filtered2sorted->preseq-c-curve input_sorted_file filtered2sorted->index_filtered_bam input_file extract_basename_2 extract_basename_2 extract_basename_1->extract_basename_2 file_path bam_idxstats bam_idxstats bam_idxstats->percent_mitochondrial_reads idxstats index_bams index_bams index_bams->bam_idxstats bam filter-unmapped filter-unmapped filter-unmapped->filtered2sorted input_file sort_dups_marked_bams->index_dups_marked_bams input_file mark_duplicates->output_picard_mark_duplicates_files mark_duplicates->sort_dups_marked_bams input_file extract_basename_2->bowtie-se output_filename extract_basename_2->execute_pcr_bottleneck_coef input_output_filenames extract_basename_2->preseq-c-curve output_file_basename extract_basename_2->filter-unmapped output_filename extract_basename_2->mark_duplicates output_filename sam2bam->sort_bams input_file sort_bams->index_bams input_file sort_bams->filter-unmapped input_file
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Inputs

ID Type Title 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 Label 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/extract-basename.cwl (CommandLineTool)

Extracts the base name of a file
extract_basename_2
../utils/remove-extension.cwl (CommandLineTool)

Extracts the base name of a file
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

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 Label 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.
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Permalink: https://w3id.org/cwl/view/git/67e8ccd5abddbd9e27f23ceeb95536fecf792d93/v1.0/ATAC-seq_pipeline/03-map-se.cwl