Index

A

abstract_step module AbstractSourceStep (class in abstract_step) AbstractStep (class in abstract_step) adapterremoval add_connection() (abstract_step.AbstractStep method) (connections_collector.ConnectionsCollector method) add_dependency() (abstract_step.AbstractStep method) add_empty() (connections_collector.ConnectionsCollector 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) add_temporary_file() (run.Run method) all_runs_have_connection() (connections_collector.ConnectionsCollector method) all_tasks_topologically_sorted (pipeline.Pipeline attribute) annotation_written (run.Run attribute) any_runs_have_connection() (connections_collector.ConnectionsCollector method) 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 bcl2fastq2_source bcl2fastq_source bowtie2

bowtie2_generate_index bwa_backtrack bwa_generate_index bwa_mem bytes_to_str() (in module misc)

C

cat_text check_required_out_connections() (abstract_step.AbstractStep method) check_tool() (in module pipeline) check_tools() (pipeline.Pipeline method) chimpipe chromhmm_binarizebam chromhmm_learnmodel collect_scs config (pipeline.Pipeline attribute) config_name (pipeline.Pipeline attribute) ConfigurationException connect() (connections_collector.ConnectionsCollector method)

connection_exists() (connections_collector.ConnectionsCollector method) connection_items() (connections_collector.ConnectionsCollector method) connections_collector module ConnectionsCollector (class in connections_collector) COPY_BLOCK_SIZE (process_pool.ProcessPool attribute) copy_file coreutils (in module pipeline) count_rRNA cuffcompare cufflinks cuffmerge cutadapt

D

declare_run() (abstract_step.AbstractStep method) deepTools_bamCompare deepTools_bamPEFragmentSize deepTools_multiBamSummary

deepTools_plotFingerprint dependencies (abstract_step.AbstractStep attribute) dependencies() (run.Run method) discardLargeSplitsAndPairs duration_to_str() (in module misc)

E

Enum (class in misc)

exists_connection_for_run() (connections_collector.ConnectionsCollector method)

F

fastq_screen fastq_source fastqc fastqsample fastx_quality_stats fastx_reverse_complement feature_counts fetch_chrom_sizes_source file_dependencies (pipeline.Pipeline attribute)

file_dependencies_reverse (pipeline.Pipeline attribute) filter_gtf finalize() (abstract_step.AbstractStep method) find_upstream_info_for_input_paths() (abstract_step.AbstractStep method) fix_cutadapt fsc (run.Run attribute) fscache module FSCache (class in fscache) fusioncatcher

G

get_cluster_job_ids() (pipeline.Pipeline method) get_connection() (connections_collector.ConnectionsCollector method) get_connections() (abstract_step.AbstractStep method) get_cores() (abstract_step.AbstractStep method) get_in_connections() (abstract_step.AbstractStep 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() (abstract_step.AbstractStep method) (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_runs() (run.Run method) get_parent_tasks() (task.Task method) get_path_tool() (abstract_step.AbstractStep 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_structure() (run.Run method) get_runs() (abstract_step.AbstractStep method) get_runs_with_any() (connections_collector.ConnectionsCollector method) get_runs_with_connections() (connections_collector.ConnectionsCollector method) get_runs_without_any() (connections_collector.ConnectionsCollector 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_for_file() (pipeline.Pipeline method) get_task_state() (task.Task method) get_task_with_list() (pipeline.Pipeline method) get_temp_output_directory() (run.Run method) get_temp_paths() (run.Run method) get_tool() (abstract_step.AbstractStep method) gffcompare_single gffread_extract_transcripts git_tag (pipeline.Pipeline attribute) gsnap

H

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

hisat2 htseq_count

I

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

is_option_set_in_config() (abstract_step.AbstractStep method) is_stale() (run.Run method) items() (connections_collector.ConnectionsCollector method)

K

kallisto kallisto_fusion kallisto_index

kill() (process_pool.ProcessPool class method) kill_all_child_processes() (process_pool.ProcessPool class method) known_config_keys (pipeline.Pipeline attribute)

L

launch() (process_pool.ProcessPool method) literal (class in misc)

log() (process_pool.ProcessPool method) look_for_unique() (connections_collector.ConnectionsCollector method)

M

macs2 merge_assembly merge_fasta_files merge_fastq_files merge_fastx_files merge_genecounts merge_numpy_zip_arrays misc module

module abstract_step connections_collector fscache misc pipeline process_pool run task move_ping_file() (task.Task method)

N

natsorted() (in module misc)

notify() (pipeline.Pipeline method)

O

output_files() (task.Task method)

output_files_for_task_id (pipeline.Pipeline attribute)

P

pear pepr pepr_postprocess picard_add_replace_read_groups picard_collectrnaseqmetrics picard_markduplicates picard_merge_sam_bam_files pipeline module Pipeline (class in pipeline)

piranha pizzly post_cufflinksSuite post_sawdust 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 reformatCigar remove_duplicate_reads_runs remove_temporary_paths() (run.Run method) require_tool() (abstract_step.AbstractStep method)

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

S

s2c salmon sam_to_fastq sam_to_sorted_bam samtools samtools_faidx samtools_index samtools_merge samtools_sort samtools_stats segemehl segemehl_2017 segemehl_generate_index segemehl_generate_index_bisulfite set_cores() (abstract_step.AbstractStep method) set_options() (abstract_step.AbstractStep method)

set_step_name() (abstract_step.AbstractStep method) setup_lmod() (pipeline.Pipeline method) sha256sum_of() (in module misc) sha_and_file() (in module misc) SIGTERM_TIMEOUT (process_pool.ProcessPool attribute) soapfuse source_controller split_fastq sra_fastq_dump star states (pipeline.Pipeline attribute) steps (pipeline.Pipeline attribute) stringtie stringtie_prepDE stringtieMerge subsetMappedReads switch_run_id() (connections_collector.ConnectionsCollector method)

T

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

tasks_in_step (pipeline.Pipeline attribute) tcount2gcount TimeoutException tophat2 topological_step_order (pipeline.Pipeline attribute) trim_galore trimmomatic type_tuple (class in misc)

U

update_public_info() (run.Run method)

used_tools (pipeline.Pipeline attribute)

V

values() (connections_collector.ConnectionsCollector method)

W

write_annotation_file() (run.Run method)