Workflow: 03-map-se-blacklist-removal.cwl
ATAC-seq 03 mapping - reads: SE - blacklist removal
- Selected
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- Default Values
- Nested Workflows
- Tools
- Inputs/Outputs
Inputs
ID | Type | Title | Doc |
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nthreads | Integer | ||
picard_jar_path | String |
Picard Java jar file |
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picard_java_opts | String (Optional) |
JVM arguments should be a quoted, space separated list (e.g. \"-Xms128m -Xmx512m\") |
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genome_sizes_file | File |
Genome sizes tab-delimited file (used in samtools) |
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input_fastq_files | File[] |
Input fastq files |
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ENCODE_blacklist_bedfile | File |
Bedfile containing ENCODE consensus blacklist regions to be excluded. |
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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)
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bowtie-se |
../map/bowtie-se.cwl
(CommandLineTool)
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sort_bams |
../map/samtools-sort.cwl
(CommandLineTool)
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index_bams |
../map/samtools-index.cwl
(CommandLineTool)
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bam_idxstats |
../map/samtools-idxstats.cwl
(CommandLineTool)
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preseq-c-curve |
../map/preseq-c_curve.cwl
(CommandLineTool)
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Usage: c_curve [OPTIONS] <sorted-bed-file> |
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filter-unmapped |
../map/samtools-filter-unmapped.cwl
(CommandLineTool)
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filtered2sorted |
../map/samtools-sort.cwl
(CommandLineTool)
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mark_duplicates |
../map/picard-MarkDuplicates.cwl
(CommandLineTool)
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sort_dedup_bams |
../map/samtools-sort.cwl
(CommandLineTool)
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index_dedup_bams |
../map/samtools-index.cwl
(CommandLineTool)
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sort_masked_bams |
../map/samtools-sort.cwl
(CommandLineTool)
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index_masked_bams |
../map/samtools-index.cwl
(CommandLineTool)
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remove_duplicates |
../map/samtools-view.cwl
(CommandLineTool)
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extract_basename_1 |
../utils/basename.cwl
(ExpressionTool)
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index_filtered_bam |
../map/samtools-index.cwl
(CommandLineTool)
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mapped_reads_count |
../map/bowtie-log-read-count.cwl
(CommandLineTool)
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Get number of processed reads from Bowtie log. |
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percent_uniq_reads |
../map/preseq-percent-uniq-reads.cwl
(CommandLineTool)
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Get number of processed reads from Bowtie log. |
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masked_file_basename |
../utils/extract-basename.cwl
(CommandLineTool)
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Extracts the base name of a file |
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sort_dups_marked_bams |
../map/samtools-sort.cwl
(CommandLineTool)
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index_dups_marked_bams |
../map/samtools-index.cwl
(CommandLineTool)
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remove_encode_blacklist |
../map/bedtools-intersect.cwl
(CommandLineTool)
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Tool: bedtools intersect (aka intersectBed)
Version: v2.25.0
Summary: Report overlaps between two feature files. |
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execute_pcr_bottleneck_coef |
../map/pcr-bottleneck-coef.cwl
(Workflow)
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ChIP-seq - map - PCR Bottleneck Coefficients |
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mapped_filtered_reads_count |
../peak_calling/samtools-extract-number-mapped-reads.cwl
(CommandLineTool)
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Extract mapped reads from BAM file using Samtools flagstat command |
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percent_mitochondrial_reads |
../utils/idxstats-percentage-of-reads-in-chrom.cwl
(ExpressionTool)
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Outputs
ID | Type | Label | Doc |
---|---|---|---|
output_pbc_files | File[] |
PCR Bottleneck Coeficient files. |
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output_bowtie_log | File[] |
Bowtie log file. |
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output_read_count_mapped | File[] |
Read counts of the mapped BAM files |
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output_preseq_c_curve_files | File[] |
Preseq c_curve output files. |
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output_percentage_uniq_reads | File[] |
Percentage of uniq reads from preseq c_curve output |
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output_read_count_mapped_filtered | File[] |
Read counts of the mapped and filtered BAM files |
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output_data_sorted_dedup_bam_files | File[] |
BAM files without duplicate reads. |
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output_percent_mitochondrial_reads | File[] |
Percentage of mitochondrial reads. |
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output_picard_mark_duplicates_files | File[] |
Picard MarkDuplicates metrics files. |
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output_data_sorted_dups_marked_bam_files | File[] |
BAM files with marked duplicate reads. |
https://w3id.org/cwl/view/git/8d02684ae0ff27e641f3704686e3bc8b1979b854/v1.0/ATAC-seq_pipeline/03-map-se-blacklist-removal.cwl