Index

A | B | C | D | F | G | H | I | K | L | M | N | O | P | R | S | T | U | W

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_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
cluster_config (pipeline.Pipeline attribute)
cluster_type (pipeline.Pipeline attribute)
config (pipeline.Pipeline attribute)
COPY_BLOCK_SIZE (process_pool.ProcessPool attribute)
cutadapt

D

declare_run() (abstract_step.AbstractStep method)
dependencies (abstract_step.AbstractStep attribute)
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)
(task.Task method)
get_annotation_for_input_file() (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_files_for_run_id_and_connection() (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() (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_and_input_files_for_connection() (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_input_file_for_connection() (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

narrowpeak_to_bed
natsorted() (in module misc)
notify() (pipeline.Pipeline method)

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)
pipeline_path (pipeline.Pipeline attribute)
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
remove_duplicate_reads_runs
remove_temporary_paths() (run.Run method)
reports() (abstract_step.AbstractStep method)
require_tool() (abstract_step.AbstractStep method)
rseqc
Run (class in run)
run (module)
run() (abstract_step.AbstractStep method)
(task.Task method)
run_folder_source
runs() (abstract_step.AbstractStep method)

S

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)
states (pipeline.Pipeline attribute)
steps (pipeline.Pipeline attribute)

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)