Index

A

abstract_step (module) AbstractSourceStep (class in abstract_step) AbstractStep (class in abstract_step) add_connection() (abstract_step.AbstractStep method) add_dependency() (abstract_step.AbstractStep method) add_empty_output_connection() (run.Run method) add_input_connection() (abstract_step.AbstractStep method) add_option() (abstract_step.AbstractStep method) add_output_connection() (abstract_step.AbstractStep method)

add_output_file() (run.Run method) add_private_info() (run.Run method) add_public_info() (run.Run method) add_temporary_directory() (run.Run method) all_tasks_topologically_sorted (pipeline.Pipeline attribute) append() (process_pool.ProcessPool.Pipeline method) append_suffix_to_path() (in module misc) assign_strings() (in module misc)

B

bam_to_bedgraph_and_bigwig bam_to_genome_browser bcl2fastq_source bowtie2 bowtie2_generate_index

bwa_backtrack bwa_generate_index bwa_mem bytes_to_str() (in module misc)

C

check_tools() (pipeline.Pipeline method) chromhmm_binarizebam chromhmm_learnmodel cluster_type (pipeline.Pipeline attribute) config (pipeline.Pipeline attribute)

COPY_BLOCK_SIZE (process_pool.ProcessPool attribute) cuffcompare cufflinks cuffmerge cutadapt

D

declare_run() (abstract_step.AbstractStep method) dependencies (abstract_step.AbstractStep attribute)

discardLargeSplitsAndPairs duration_to_str() (in module misc)

F

fastq_source fastqc fastx_quality_stats fetch_chrom_sizes_source file_dependencies (pipeline.Pipeline attribute) file_dependencies_reverse (pipeline.Pipeline attribute)

finalize() (abstract_step.AbstractStep method) find_upstream_info_for_input_paths() (abstract_step.AbstractStep method) fix_cutadapt FSCache (class in fscache) fscache (module)

G

generate_one_report() (abstract_step.AbstractStep method) generate_report() (abstract_step.AbstractStep method) get_basic_state() (run.Run method) get_cores() (abstract_step.AbstractStep method) get_execution_hashtag() (run.Run method) get_in_connections() (abstract_step.AbstractStep method) get_input_files_for_output_file() (run.Run method) get_input_runs() (abstract_step.AbstractStep method) get_log() (process_pool.ProcessPool method) get_module_loads() (abstract_step.AbstractStep method) get_module_unloads() (abstract_step.AbstractStep method) get_option() (abstract_step.AbstractStep method) get_options() (abstract_step.AbstractStep method) get_out_connections() (abstract_step.AbstractStep method) get_output_directory() (run.Run method) get_output_directory_du_jour() (run.Run method) get_output_directory_du_jour_placeholder() (run.Run method) get_output_files_abspath() (run.Run method) get_output_files_for_annotation_and_tags() (run.Run method) get_parent_tasks() (task.Task method) get_pipeline() (task.Task method)

get_post_commands() (abstract_step.AbstractStep method) get_pre_commands() (abstract_step.AbstractStep method) get_private_info() (run.Run method) get_public_info() (run.Run method) get_run() (abstract_step.AbstractStep method) (task.Task method) get_run_ids() (abstract_step.AbstractStep method) get_run_ids_in_connections_input_files() (abstract_step.AbstractStep method) get_run_ids_out_connections_output_files() (abstract_step.AbstractStep method) get_run_state() (abstract_step.AbstractStep method) get_run_state_basic() (abstract_step.AbstractStep method) get_runs() (abstract_step.AbstractStep method) get_single_output_file_for_annotation() (run.Run method) get_step() (task.Task method) get_step_class_for_key() (abstract_step.AbstractStep class method) get_step_name() (abstract_step.AbstractStep method) get_step_type() (abstract_step.AbstractStep method) get_task_state() (task.Task method) get_task_state_basic() (task.Task method) get_temp_output_directory() (run.Run method) get_tool() (abstract_step.AbstractStep method)

H

has_private_info() (run.Run method) has_public_info() (run.Run method)

htseq_count

I

input_files() (task.Task method) input_files_for_task_id (pipeline.Pipeline attribute)

is_option_set_in_config() (abstract_step.AbstractStep method)

K

kill() (process_pool.ProcessPool class method)

kill_all_child_processes() (process_pool.ProcessPool class method)

L

launch() (process_pool.ProcessPool method)

log() (process_pool.ProcessPool method)

M

macs2 merge_fasta_files

merge_fastq_files misc (module)

N

natsorted() (in module misc)

O

output_files() (task.Task method)

output_files_for_task_id (pipeline.Pipeline attribute)

P

picard_add_replace_read_groups picard_markduplicates picard_merge_sam_bam_files Pipeline (class in pipeline) pipeline (module) post_cufflinksSuite

preseq_complexity_curve preseq_future_genome_coverage preseq_future_yield process_pool (module) ProcessPool (class in process_pool) ProcessPool.Pipeline (class in process_pool)

R

raw_file_source raw_file_sources raw_url_source raw_url_sources remove_duplicate_reads_runs remove_temporary_paths() (run.Run method) reports() (abstract_step.AbstractStep method) require_tool() (abstract_step.AbstractStep method)

rgt_thor rseqc Run (class in run) run (module) run() (abstract_step.AbstractStep method) (task.Task method) run_folder_source runs() (abstract_step.AbstractStep method)

S

s2c sam_to_sorted_bam samtools_faidx samtools_index samtools_stats segemehl segemehl_generate_index set_cores() (abstract_step.AbstractStep method)

set_options() (abstract_step.AbstractStep method) set_step_name() (abstract_step.AbstractStep method) SIGTERM_TIMEOUT (process_pool.ProcessPool attribute) sra_fastq_dump states (pipeline.Pipeline attribute) steps (pipeline.Pipeline attribute) subsetMappedReads

T

TAIL_LENGTH (process_pool.ProcessPool attribute) Task (class in task) task (module) task_for_task_id (pipeline.Pipeline attribute)

task_id_for_output_file (pipeline.Pipeline attribute) task_ids_for_input_file (pipeline.Pipeline attribute) tophat2 topological_step_order (pipeline.Pipeline attribute)

U

update_public_info() (run.Run method)

W

write_annotation_file() (run.Run method)