{"@id":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"81555a89cc2d16bd3ab131a6685a44b44f08f927","path":"v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl"},"retrievedOn":"2026-09-21T16:00:03.343+00:00","lastCommit":"81555a89cc2d16bd3ab131a6685a44b44f08f927","label":"pipeline-pe-blacklist-removal.cwl","doc":"ATAC-seq pipeline - reads: PE - with blacklist removal","inputs":{"nthreads_qc":{"doc":"Number of threads required for the 01-qc step","type":"Integer"},"nthreads_map":{"doc":"Number of threads required for the 03-map step","type":"Integer"},"nthreads_quant":{"doc":"Number of threads required for the 05-quantification step","type":"Integer"},"nthreads_trimm":{"doc":"Number of threads required for the 02-trim step","type":"Integer"},"picard_jar_path":{"doc":"Picard Java jar file","type":"String"},"picard_java_opts":{"doc":"JVM arguments should be a quoted, space separated list (e.g. \\\"-Xms128m -Xmx512m\\\")","type":"String (Optional)"},"genome_sizes_file":{"doc":"Genome sizes tab-delimited file (used in samtools)","type":"File"},"nthreads_peakcall":{"doc":"Number of threads required for the 04-peakcall step","type":"Integer"},"as_narrowPeak_file":{"doc":"Definition narrowPeak file in AutoSql format (used in bedToBigBed)","type":"File"},"trimmomatic_jar_path":{"doc":"Trimmomatic Java jar file","type":"String"},"default_adapters_file":{"doc":"Adapters file","type":"File"},"genome_effective_size":{"doc":"Effective genome size used by MACS2. 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- Quantification","run":"05-quantification.cwl","runType":"WORKFLOW","sources":{"quant":{"sourceIDs":["map"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl#quant/nthreads":{"sourceIDs":["nthreads_quant"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl#quant/input_genome_sizes":{"sourceIDs":["genome_sizes_file"]}}},"trimm":{"doc":"ATAC-seq 02 trimming - reads: 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\"input_fastq_read2_files\" -> \"trimm\" [label=\"input_read2_fastq_files\"];\n  \"genome_ref_first_index_file\" -> \"map\" [label=\"genome_ref_first_index_file\"];\n  \"picard_jar_path\" -> \"map\" [label=\"picard_jar_path\"];\n  \"picard_java_opts\" -> \"map\" [label=\"picard_java_opts\"];\n  \"ENCODE_blacklist_bedfile\" -> \"map\" [label=\"ENCODE_blacklist_bedfile\"];\n  \"trimm\" -> \"map\" [label=\"input_fastq_read1_files\"];\n  \"nthreads_map\" -> \"map\" [label=\"nthreads\"];\n  \"genome_sizes_file\" -> \"map\" [label=\"genome_sizes_file\"];\n  \"trimm\" -> \"map\" [label=\"input_fastq_read2_files\"];\n  \"map\" -> \"peak_call\" [label=\"input_bam_files\"];\n  \"genome_effective_size\" -> \"peak_call\" [label=\"genome_effective_size\"];\n  \"nthreads_peakcall\" -> \"peak_call\" [label=\"nthreads\"];\n  \"as_narrowPeak_file\" -> \"peak_call\" [label=\"as_narrowPeak_file\"];\n  \"genome_sizes_file\" -> \"peak_call\" [label=\"input_genome_sizes\"];\n  \"nthreads_qc\" -> \"qc\" [label=\"nthreads\"];\n  \"input_fastq_read1_files\" -> \"qc\" [label=\"input_read1_fastq_files\"];\n  \"input_fastq_read2_files\" -> \"qc\" [label=\"input_read2_fastq_files\"];\n  \"default_adapters_file\" -> \"qc\" [label=\"default_adapters_file\"];\n  \"map\" -> \"quant\" [label=\"input_bam_files\"];\n  \"genome_sizes_file\" -> \"quant\" [label=\"input_genome_sizes\"];\n  \"nthreads_quant\" -> \"quant\" [label=\"nthreads\"];\n  \"map\" -> \"map_dedup_bam_files\";\n  \"peak_call\" -> \"peakcall_output_unpaired_peak_summits_file\";\n  \"quant\" -> \"quant_bigwig_raw_files\";\n  \"map\" -> \"map_pbc_files\";\n  \"peak_call\" -> \"peakcall_output_unpaired_peak_file\";\n  \"peak_call\" -> \"peakcall_output_unpaired_peak_bigbed_file\";\n  \"qc\" -> \"qc_fastqc_report_files_read2\";\n  \"map\" -> \"map_read_count_mapped\";\n  \"qc\" -> \"qc_diff_counts_read2\";\n  \"peak_call\" -> \"peakcall_peak_bigbed_file\";\n  \"map\" -> \"map_preseq_c_curve_files\";\n  \"peak_call\" -> \"peakcall_peak_count_within_replicate\";\n  \"qc\" -> \"qc_count_raw_reads_read2\";\n  \"map\" -> \"map_percent_mitochondrial_reads\";\n  \"qc\" -> \"qc_diff_counts_read1\";\n  \"trimm\" -> \"trimm_fastq_files_read2\";\n  \"peak_call\" -> \"peakcall_output_unpaired_peak_count_within_replicate\";\n  \"map\" -> \"map_preseq_percentage_uniq_reads\";\n  \"peak_call\" -> \"peakcall_output_unpaired_extended_peak_file\";\n  \"peak_call\" -> \"peakcall_extended_peak_file\";\n  \"peak_call\" -> \"peakcall_output_unpaired_peak_xls_file\";\n  \"quant\" -> \"quant_bigwig_norm_files\";\n  \"peak_call\" -> \"peakcall_output_unpaired_filtered_read_count_file\";\n  \"qc\" -> \"qc_count_raw_reads_read1\";\n  \"peak_call\" -> \"peakcall_filtered_read_count_file\";\n  \"peak_call\" -> \"peakcall_spp_x_cross_corr\";\n  \"qc\" -> \"qc_fastqc_data_files_read1\";\n  \"qc\" -> \"qc_fastqc_data_files_read2\";\n  \"peak_call\" -> \"peakcall_spp_x_cross_corr_plot\";\n  \"trimm\" -> \"trimm_raw_counts_read2\";\n  \"peak_call\" -> \"peakcall_peak_file\";\n  \"trimm\" -> \"trimm_fastq_files_read1\";\n  \"peak_call\" -> \"peakcall_peak_xls_file\";\n  \"qc\" -> \"qc_fastqc_report_files_read1\";\n  \"map\" -> \"map_bowtie_log_files\";\n  \"peak_call\" -> \"peakcall_read_in_peak_count_within_replicate\";\n  \"peak_call\" -> \"peakcall_peak_summits_file\";\n  \"map\" -> \"map_mark_duplicates_files\";\n  \"trimm\" -> \"trimm_raw_counts_read1\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","visualisationPng":"/graph/png/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","visualisationSvg":"/graph/svg/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","roBundle":"/robundle/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/pipeline-pe-blacklist-removal.cwl","licenseName":"MIT License"}