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using networkx to create a simple graph
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| import networkx as nx | |
| import matplotlib.pyplot as plt | |
| def draw_graph(graph, labels=None, graph_layout='shell', | |
| node_size=1600, node_color='blue', node_alpha=0.3, | |
| node_text_size=12, | |
| edge_color='blue', edge_alpha=0.3, edge_tickness=1, | |
| edge_text_pos=0.3, | |
| text_font='sans-serif'): | |
| # create networkx graph | |
| G=nx.Graph() | |
| # add edges | |
| for edge in graph: | |
| G.add_edge(edge[0], edge[1]) | |
| # these are different layouts for the network you may try | |
| # shell seems to work best | |
| if graph_layout == 'spring': | |
| graph_pos=nx.spring_layout(G) | |
| elif graph_layout == 'spectral': | |
| graph_pos=nx.spectral_layout(G) | |
| elif graph_layout == 'random': | |
| graph_pos=nx.random_layout(G) | |
| else: | |
| graph_pos=nx.shell_layout(G) | |
| # draw graph | |
| nx.draw_networkx_nodes(G,graph_pos,node_size=node_size, | |
| alpha=node_alpha, node_color=node_color) | |
| nx.draw_networkx_edges(G,graph_pos,width=edge_tickness, | |
| alpha=edge_alpha,edge_color=edge_color) | |
| nx.draw_networkx_labels(G, graph_pos,font_size=node_text_size, | |
| font_family=text_font) | |
| if labels is None: | |
| labels = range(len(graph)) | |
| edge_labels = dict(zip(graph, labels)) | |
| nx.draw_networkx_edge_labels(G, graph_pos, edge_labels=edge_labels, | |
| label_pos=edge_text_pos) | |
| # show graph | |
| plt.show() | |
| graph = [(0, 1), (1, 5), (1, 7), (4, 5), (4, 8), (1, 6), (3, 7), (5, 9), | |
| (2, 4), (0, 4), (2, 5), (3, 6), (8, 9)] | |
| # you may name your edge labels | |
| labels = map(chr, range(65, 65+len(graph))) | |
| #draw_graph(graph, labels) | |
| # if edge labels is not specified, numeric labels (0, 1, 2...) will be used | |
| draw_graph(graph) |
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| __PIPELINE_INFO__: | |
| name: miseq_discovery_version | |
| version: '1.7' | |
| author: 'Rad' | |
| data_type: null | |
| input_type: 'fastq, tsv' | |
| output_type: 'bam, tsv, vcf' | |
| host_cluster: 'genesis' | |
| date_created: '' | |
| date_last_updated: 'Feb 5, 2015' | |
| factory_version: '1.10.1' | |
| __GENERAL__: | |
| python: 'path to python binary' | |
| java: 'path to java 1.7 binary' | |
| bowtie2: 'path to bowtie2 binary' | |
| gatk: 'path to GATK v 3.1.1 binary' | |
| picard: 'path to picard tool AddOrReplaceReadGroups binary' | |
| R: null | |
| mutationseq: 'path to mutation seq' | |
| __SHARED__: | |
| ref_genome: 'path to the root directory of the reference genome' | |
| ref_genome_fa: 'path to the fasta file of the reference genome' | |
| normal_fastq_file_1: 'path to the normal sample forward fastq file' | |
| normal_fastq_file_2: 'path to the normal sample reverse fastq file' | |
| dbsnp: 'path to the vcf file of dbsnp138' | |
| combined_vcfs: 'path to a file you choose to contain combined vcf calls for all the samples' | |
| combination_log: 'path to a file you choose to contain the logs of combining vcf files' | |
| amplicons_targets: 'path to the amplicon targets file, containing chromosome, start and end of each amplicon' | |
| number_of_samples: 'number of samples to be analyzed' | |
| ld_library_path: 'path to the shared library path' | |
| __SAMPLES__: | |
| sample_name: | |
| fastq_file_1: 'path to the forward fastq file' | |
| fastq_file_2: 'path to the reverse fastq file' | |
| sample_id: 'sample_name' | |
| __TASK_1__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_bowtie2' | |
| component_version: '1.0.0' | |
| seed_version: '2.0.0-beta7' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| seq2: ('__SHARED__','normal_fastq_file_2') | |
| seq1: ('__SHARED__','normal_fastq_file_1') | |
| reference: ('__SHARED__','ref_genome') | |
| output_files: | |
| outfile: 'alignment/normal.bam' | |
| parameters: | |
| __TASK_2__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'reheader' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| infile: ('__TASK_1__','outfile') | |
| output_files: | |
| outfile: 'reheaded/normal_reheaded.bam' | |
| parameters: | |
| __TASK_3__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_sort' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_2__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_2__','outfile') | |
| output_files: | |
| output: 'reheaded/normal.sorted.bam' | |
| parameters: | |
| options: '__OPTIONAL__' | |
| __TASK_4__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_index' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_3__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_3__','output') | |
| output_files: | |
| parameters: | |
| __TASK_5__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'create_targets' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_4__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| indexed_bam: null | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_3__','output') | |
| output_files: | |
| outfile: 'intervals/normal_positions.intervals' | |
| parameters: | |
| __TASK_6__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'realign' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_4__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| sorted_alignment: ('__TASK_3__','output') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_5__','outfile') | |
| output_files: | |
| outfile: 'realignment/normal_realigned.bam' | |
| parameters: | |
| __TASK_7__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'base_quality_recalibrator_pre' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| dbsnp: ('__SHARED__','dbsnp') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_6__','outfile') | |
| output_files: | |
| outfile: 'realignment/normal_score.grp' | |
| parameters: | |
| __TASK_8__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'base_quality_recalibrator_post' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| dbsnp: ('__SHARED__','dbsnp') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| bqsr: ('__TASK_7__','outfile') | |
| infile: ('__TASK_6__','outfile') | |
| output_files: | |
| outfile: 'realignment/normal_score.grp2' | |
| parameters: | |
| __TASK_9__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'print_reads' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| bqsr: ('__TASK_7__','outfile') | |
| infile: ('__TASK_6__','outfile') | |
| output_files: | |
| outfile: 'realignment/normal_recalibrated.bam' | |
| parameters: | |
| __TASK_10__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_sort' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_9__','outfile') | |
| output_files: | |
| output: 'realignment/normal_recalibrated.sorted.bam' | |
| parameters: | |
| options: null | |
| __TASK_11__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_index' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_10__','output') | |
| output_files: | |
| parameters: | |
| __TASK_12__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_bowtie2' | |
| component_version: '1.0.0' | |
| seed_version: '2.0.0-beta7' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_11__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| seq2: ('__SAMPLES__','fastq_file_2') | |
| seq1: ('__SAMPLES__','fastq_file_1') | |
| reference: ('__SHARED__','ref_genome') | |
| output_files: | |
| outfile: 'alignment/${sample_id}.bam' | |
| parameters: | |
| __TASK_13__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'reheader' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| infile: ('__TASK_12__','outfile') | |
| output_files: | |
| outfile: 'reheaded/${sample_id}_reheaded.bam' | |
| parameters: | |
| __TASK_14__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_sort' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_13__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_13__','outfile') | |
| output_files: | |
| output: 'reheaded/${sample_id}.sorted.bam' | |
| parameters: | |
| options: '__OPTIONAL__' | |
| __TASK_15__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_index' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_14__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_14__','output') | |
| output_files: | |
| parameters: | |
| __TASK_16__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'create_targets' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_15__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| indexed_bam: null | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_14__','output') | |
| output_files: | |
| outfile: 'intervals/${sample_id}_positions.intervals' | |
| parameters: | |
| __TASK_17__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'realign' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_14__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| sorted_alignment: ('__TASK_14__','output') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_16__','outfile') | |
| output_files: | |
| outfile: 'realignment/${sample_id}_realigned.bam' | |
| parameters: | |
| __TASK_18__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'base_quality_recalibrator_pre' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| dbsnp: ('__SHARED__','dbsnp') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| infile: ('__TASK_17__','outfile') | |
| output_files: | |
| outfile: 'realignment/${sample_id}_score.grp' | |
| parameters: | |
| __TASK_19__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'base_quality_recalibrator_post' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| dbsnp: ('__SHARED__','dbsnp') | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| bqsr: ('__TASK_18__','outfile') | |
| infile: ('__TASK_17__','outfile') | |
| output_files: | |
| outfile: 'realignment/${sample_id}_score.grp2' | |
| parameters: | |
| __TASK_20__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'print_reads' | |
| component_version: '1.0.0' | |
| seed_version: '3.1.1' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| ref_genome: ('__SHARED__','ref_genome_fa') | |
| bqsr: ('__TASK_18__','outfile') | |
| infile: ('__TASK_17__','outfile') | |
| output_files: | |
| outfile: 'realignment/${sample_id}_recalibrated.bam' | |
| parameters: | |
| __TASK_21__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_sort' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_20__','outfile') | |
| output_files: | |
| output: 'realignment/${sample_id}_recalibrated.sorted.bam' | |
| parameters: | |
| options: '__OPTIONAL__' | |
| __TASK_22__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_samtools_index' | |
| component_version: '1.0.0' | |
| seed_version: '0.1.19' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input: ('__TASK_21__','output') | |
| output_files: | |
| parameters: | |
| __TASK_23__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'run_mutationseq' | |
| component_version: '1.0.3' | |
| seed_version: '4.3.3' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_22__'] | |
| add_breakpoint: False | |
| env_vars: | |
| PATH: '/genesis/extscratch/shahlab/raniba/pipelines/miseq_pipeline/miseq_analysis_pipeline/miseq-pipeline/software/samtools-0.1.19/' | |
| LD_LIBRARY_PATH: ['/genesis/extscratch/shahlab/raniba/pipelines/miseq_pipeline/miseq_analysis_pipeline/miseq-pipeline/software/Python-2.7.6/lib'] | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| tumour: ('__TASK_21__','output') | |
| reference: ('__SHARED__','ref_genome_fa') | |
| positions_file: null | |
| normal: ('__TASK_10__','output') | |
| model: 'model_deep_v0.2.npz' | |
| config: 'metadata.config' | |
| output_files: | |
| export_features: null | |
| out: 'calls/${sample_id}_mutationseq.vcf' | |
| log_file: '../logs/mutationSeq_run.log' | |
| parameters: | |
| all: '__FLAG__' | |
| features_only: '__FLAG__' | |
| verbose: '__FLAG__' | |
| normal_variant: 25 | |
| interval: null | |
| titan_mode: '__FLAG__' | |
| deep: True | |
| no_filter: '__FLAG__' | |
| manifest: ('__SHARED__','amplicons_targets') | |
| tumour_variant: 2 | |
| single: False | |
| normalized: '__FLAG__' | |
| coverage: 4 | |
| return_cov: '__FLAG__' | |
| threshold: 0.5 | |
| buffer_size: '2G' | |
| baseq_threshold: 10 | |
| mapq_threshold: 20 | |
| purity: 70 | |
| __TASK_24__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'combine_vcfs' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_23__'] | |
| add_breakpoint: True | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| input_vcf: ('__TASK_23__','out') | |
| sample_id: ('__SAMPLES__','sample_id') | |
| combined_vcfs: ('__SHARED__','combined_vcfs') | |
| combination_log: ('__SHARED__','combination_log') | |
| output_files: | |
| outfile: '__OPTIONAL__' | |
| parameters: | |
| __TASK_25__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'create_positions' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_24__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| component: | |
| input_files: | |
| amplicons_targets: ('__SHARED__','amplicons_targets') | |
| infile: ('__SHARED__','combined_vcfs') | |
| output_files: | |
| outfile: 'positions/${sample_id}_positions.tsv' | |
| parameters: | |
| log_dump: ('__SHARED__','combination_log') | |
| number_of_samples: ('__SHARED__','number_of_samples') | |
| __TASK_26__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'build_amplicon_positions' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_25__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| variant_positions: ('__TASK_25__','outfile') | |
| output_files: | |
| amplicon_positions: 'positions/${sample_id}_amplicons_positions.tsv' | |
| parameters: | |
| __TASK_27__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'build_count_files' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: ['__TASK_26__', '__TASK_22__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| sorted_bam: ('__TASK_21__','output') | |
| ref_genome: ('__SHARED__', 'ref_genome_fa') | |
| amplicon_positions: ('__TASK_26__','amplicon_positions') | |
| indexed_bam: null | |
| output_files: | |
| counts_file: 'counts/${sample_id}_counts.tsv' | |
| parameters: | |
| min_mqual: 10 | |
| min_bqual: 20 | |
| __TASK_28__: | |
| reserved: | |
| # do not change this section | |
| component_name: 'do_binomial_exact_test' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_27__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: null | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: null | |
| component: | |
| input_files: | |
| counts_file: ('__TASK_27__','counts_file') | |
| variant_positions: ('__TASK_25__','outfile') | |
| output_files: | |
| variant_status: 'variant_status/${sample_id}_variant_status.tsv' | |
| parameters: | |
| low_coverage_threshold: 50 | |
| family_wise_error_rate: 0.001 | |
| variant_call_files_log: ('__SHARED__', 'snv_calls') | |
| sample_ids_log: ('__SHARED__', 'snv_calls_ids') | |
| __TASK_29__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'run_strelka' | |
| component_version: '1.2.0' | |
| seed_version: '1.0.13' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: | |
| component: | |
| input_files: | |
| tumor: ('__TASK_21__', 'output') | |
| config: '__OPTIONAL__' | |
| ref: ('__SHARED__','strelka_ref') | |
| normal: ('__TASK_10__', 'output') | |
| output_files: | |
| output_dir: strelka_output | |
| parameters: | |
| num_procs: 8 | |
| isSkipDepthFilters: ('__SHARED__','isSkipDepthFilters') | |
| __TASK_30__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'run_snpeff' | |
| component_version: '1.0.2' | |
| seed_version: 'SnpEff 3.6b (build 2014-05-01)' | |
| run: | |
| use_cluster: True | |
| memory: '4G' | |
| forced_dependencies: ['__TASK_29__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: | |
| component: | |
| input_files: | |
| variants_file: passed.somatic.snvs.vcf | |
| config: 'snpEff_3_6/snpEff.config' | |
| output_files: | |
| stats: 'snpEff_summary.html' | |
| out: 'strelka.passed.somatic.snvs.annotSnpEff.vcf' | |
| parameters: | |
| upDownStreamLen: '__OPTIONAL__' | |
| verbose: '__FLAG__' | |
| cancer: '__FLAG__' | |
| treatAllAsProteinCoding: '__OPTIONAL__' | |
| one: '__FLAG__' | |
| dataDir: '__OPTIONAL__' | |
| 'no': '__OPTIONAL__' | |
| outOffset: '__FLAG__' | |
| help: '__FLAG__' | |
| het: '__FLAG__' | |
| oicr: '__FLAG__' | |
| lof: '__FLAG__' | |
| no_utr: '__FLAG__' | |
| minC: '__OPTIONAL__' | |
| sequenceOntology: '__FLAG__' | |
| chr: '__OPTIONAL__' | |
| around: '__FLAG__' | |
| output_format: 'vcf' | |
| cvsStats: '__FLAG__' | |
| no_intergenic: '__FLAG__' | |
| noLog: '__FLAG__' | |
| noStats: True | |
| del: '__FLAG__' | |
| debug: '__FLAG__' | |
| motif: '__FLAG__' | |
| input_format: 'vcf' | |
| maxQ: '__OPTIONAL__' | |
| canon: '__FLAG__' | |
| ins: '__FLAG__' | |
| zero: '__FLAG__' | |
| genome_version: 'GRCh37.66' | |
| no_intron: '__FLAG__' | |
| download: '__FLAG__' | |
| maxC: '__OPTIONAL__' | |
| cancerSamples: '__OPTIONAL__' | |
| hom: '__FLAG__' | |
| no_downstream: '__FLAG__' | |
| hgvs: '__FLAG__' | |
| minQ: '__OPTIONAL__' | |
| reg: '__OPTIONAL__' | |
| geneId: '__FLAG__' | |
| onlyReg: '__FLAG__' | |
| nmp: '__FLAG__' | |
| threads: '__OPTIONAL__' | |
| snp: '__FLAG__' | |
| no_upstream: '__FLAG__' | |
| interval: '__OPTIONAL__' | |
| quiet: '__FLAG__' | |
| filterInterval: '__OPTIONAL__' | |
| inOffset: '__FLAG__' | |
| __TASK_30a__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'annot_mutationassessor_vcf' | |
| component_version: '1.0.0' | |
| seed_version: '1.0.0' | |
| run: | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| parallel_run: False | |
| parallel_params: ['vcf'] | |
| interval_file: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'mutation_assessor_db') | |
| vcf: ('__TASK_30__', 'out') | |
| output_files: | |
| output: strelka.passed.somatic.snvs.annotSnpEff.annotMA.vcf | |
| parameters: | |
| __TASK_31__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'dbsnp') | |
| infile: ('__TASK_30a__', 'output') | |
| output_files: | |
| out: strelka.passed.somatic.snvs.annotSnpEff.annotMA.flagDBsnp.vcf | |
| parameters: | |
| label: DBSNP | |
| flag_with_id: True | |
| input_type: 'snv' | |
| __TASK_32__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'thousand_genomes') | |
| infile: ('__TASK_31__', 'out') | |
| output_files: | |
| out: 'strelka.passed.somatic.snvs.annotSnpEff.annotMA.flagDBsnp.flag1000gen.vcf' | |
| parameters: | |
| label: 1000Gen | |
| flag_with_id: '__FLAG__' | |
| input_type: 'snv' | |
| __TASK_32a__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'cosmic_db') | |
| infile: ('__TASK_32__', 'out') | |
| output_files: | |
| out: 'results/${sample_id}_strelka.passed.somatic.snvs.annotSnpEff.annotMA.flagDBsnp.flag1000gen.flagCosmic.vcf' | |
| parameters: | |
| label: Cosmic | |
| flag_with_id: True | |
| input_type: 'snv' | |
| __TASK_33__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'run_snpeff' | |
| component_version: '1.0.2' | |
| seed_version: 'SnpEff 3.6b (build 2014-05-01)' | |
| run: | |
| use_cluster: True | |
| memory: '5G' | |
| forced_dependencies: ['__TASK_29__'] | |
| add_breakpoint: False | |
| env_vars: | |
| boilerplate: | |
| parallel_run: False | |
| parallel_params: [] | |
| interval_file: | |
| component: | |
| input_files: | |
| variants_file: passed.somatic.indels.vcf | |
| config: 'snpEff_3_6/snpEff.config' | |
| output_files: | |
| stats: 'snpEff_summary.html' | |
| out: 'strelka.passed.somatic.indels.annotSnpEff.vcf' | |
| parameters: | |
| upDownStreamLen: '__OPTIONAL__' | |
| verbose: '__FLAG__' | |
| cancer: '__FLAG__' | |
| treatAllAsProteinCoding: '__OPTIONAL__' | |
| one: '__FLAG__' | |
| dataDir: '__OPTIONAL__' | |
| 'no': '__OPTIONAL__' | |
| outOffset: '__FLAG__' | |
| help: '__FLAG__' | |
| het: '__FLAG__' | |
| oicr: '__FLAG__' | |
| lof: '__FLAG__' | |
| no_utr: '__FLAG__' | |
| minC: '__OPTIONAL__' | |
| sequenceOntology: '__FLAG__' | |
| chr: '__OPTIONAL__' | |
| around: '__FLAG__' | |
| output_format: 'vcf' | |
| cvsStats: '__FLAG__' | |
| no_intergenic: '__FLAG__' | |
| noLog: '__FLAG__' | |
| noStats: True | |
| del: '__FLAG__' | |
| debug: '__FLAG__' | |
| motif: '__FLAG__' | |
| input_format: 'vcf' | |
| maxQ: '__OPTIONAL__' | |
| canon: '__FLAG__' | |
| ins: '__FLAG__' | |
| zero: '__FLAG__' | |
| genome_version: 'GRCh37.66' | |
| no_intron: '__FLAG__' | |
| download: '__FLAG__' | |
| maxC: '__OPTIONAL__' | |
| cancerSamples: '__OPTIONAL__' | |
| hom: '__FLAG__' | |
| no_downstream: '__FLAG__' | |
| hgvs: '__FLAG__' | |
| minQ: '__OPTIONAL__' | |
| reg: '__OPTIONAL__' | |
| geneId: '__FLAG__' | |
| onlyReg: '__FLAG__' | |
| nmp: '__FLAG__' | |
| threads: '__OPTIONAL__' | |
| snp: '__FLAG__' | |
| no_upstream: '__FLAG__' | |
| interval: '__OPTIONAL__' | |
| quiet: '__FLAG__' | |
| filterInterval: '__OPTIONAL__' | |
| inOffset: '__FLAG__' | |
| __TASK_34__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'dbsnp') | |
| infile: ('__TASK_33__', 'out') | |
| output_files: | |
| out: strelka.passed.somatic.indels.annotSnpEff.annotMA.flagDBsnp.vcf | |
| parameters: | |
| label: DBSNP | |
| flag_with_id: True | |
| input_type: 'indel' | |
| __TASK_35__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'thousand_genomes') | |
| infile: ('__TASK_34__', 'out') | |
| output_files: | |
| out: 'strelka.passed.somatic.indels.annotSnpEff.annotMA.flagDBsnp.flag1000gen.vcf' | |
| parameters: | |
| label: 1000Gen | |
| flag_with_id: '__FLAG__' | |
| input_type: 'indel' | |
| __TASK_35a__: | |
| reserved: | |
| # do not change this section. | |
| component_name: 'flag_positions_vcf' | |
| component_version: '1.0.3' | |
| seed_version: '1.2.0' | |
| run: | |
| # NOTE: component cannot run in parallel mode. | |
| use_cluster: True | |
| memory: '10G' | |
| forced_dependencies: [] | |
| add_breakpoint: False | |
| env_vars: | |
| LD_LIBRARY_PATH: ('__SHARED__', 'ld_library_path') | |
| boilerplate: | |
| component: | |
| input_files: | |
| db: ('__SHARED__', 'cosmic_db') | |
| infile: ('__TASK_35__', 'out') | |
| output_files: | |
| out: 'results/${sample_id}_strelka.passed.somatic.indels.annotSnpEff.annotMA.flagDBsnp.flag1000gen.flagCosmic.vcf' | |
| parameters: | |
| label: Cosmic | |
| flag_with_id: True | |
| input_type: 'indel' |
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