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000-fixme-cleanup tests/cleanup: Move failing test to other directory May 30, 2017
001-fixme-multi_with_config tests/multi_with_config: Move failing test to other directory May 30, 2017
abspath_preserve fix preserve not resolving files specified by different absolute / re… May 10, 2014
accompanies fix regression causing cleanup test to fail Jan 11, 2014
alias fix alias tests failing due to removal of 'forward to' syntax May 25, 2015
alias_cleanup fix alias tests failing due to removal of 'forward to' syntax May 25, 2015
alias_produce update test to use new alias syntax Jul 18, 2015
append_output_dir fix branch directories set in consecutive stages incorrectly nesting Aug 15, 2017
background fixed ampersands used to terminate exec commands causing bash errors Dec 23, 2012
backtick Issue 32: Forward not working inside Transform / Filter / Produce Jun 1, 2012
bed support for reading regions from BED file Jul 30, 2017
branch_dir fix branch directories set in consecutive stages incorrectly nesting Aug 15, 2017
branch_dir_from_input fix branch directories set in consecutive stages incorrectly nesting Aug 15, 2017
branch_input_before_original fix parallel branches created from file pattern split not using split… Mar 15, 2013
branch_load Reformatting and summarizing of errors at end of pipeline to make it … Feb 13, 2015
branch_variable support accessing branch variables directly, without prefix "branch." Nov 28, 2013
branch_variable_as_param fix test giving fail status even though it passes Jun 12, 2014
branch_variable_output add test for pipeline output used in branch variable Jul 20, 2014
branch_variable_override_default_param fix branch variable not overriding default value of variable specifie… Sep 13, 2014
check change test to send to file instead of gmail May 11, 2015
check_fail_issue_102 Issue #175: non-unique file for check state contam res. b/w branches Jun 4, 2016
check_no_otherwise fix test failing when checks listed in different order Aug 27, 2017
check_with_send_report support for setting check message without failing or succeeding Feb 23, 2014
chr_in_nested regression test for referenceh to chr in nested seg Jul 15, 2016
chr_region support genomes without 'chr' prefix (see #182) Sep 28, 2016
cleanup_in_pipeline support for cleanup as command in pipeline stage Jan 18, 2015
cleanup_multi test for cleaning up 2nd and later outputs Jun 13, 2014
cleanup_output_dir delete editor tmp file May 11, 2015
cleanup_output_from_ext fix test not returning true & thus failing Mar 20, 2013
cmd_line_load support for option to load libs from cmd line Aug 1, 2016
cmdlinevars add run permissions May 11, 2015
config_params support for bpipe.config parameters section May 22, 2018
consecutive_parallel Issue 53: Consecutive parallel segments cause unexpected multiple exe… Aug 12, 2012
custom_chr Fixed incorrect number of outputs mentioned in error message in some … Nov 9, 2013
define Issue 17: Composable Pipelines - Ability to Define Reusable Pipeline … Mar 9, 2012
dependent_modules support for multiple paths in BPIPE_LIB Jun 27, 2013
documentation fixed bad check in documentation test May 26, 2012
double_check regression test for check result leak between branches Oct 4, 2015
double_input_ext added various tests Mar 10, 2014
double_parallel made test more flexible to allow for allowable variation in outputs used Mar 17, 2013
downstream_multiinputs Fix: downstream references to inputs by index throwing "expected more… Jan 6, 2015
embedded_config support for embedding config inside pipeline scripts Jun 8, 2017
empty_parallel_segment fix empty_parallel_segment test hanging forever Jul 16, 2016
equal_timestamps_cleanup fix merge conflicts Dec 14, 2014
error_on_load change to make error in loaded script terminate pipeline Oct 18, 2017
extensions fix test failing due to change in wording of error message May 25, 2015
external_error Fix incorrect file reported for errors when multiple external files l… Sep 14, 2014
external_segment fixed segments with multiple parts printing incorrect names for pipel… May 29, 2012
externalstages test for from matching more than 1 input May 27, 2012
filter added cleanup script for test Aug 11, 2013
filter_annot_with_diff_input fix for incorrect input inferred by filter if actual input used diffe… May 17, 2013
filter_input_ext fix test failing due to feature of inferring outputs removed Apr 20, 2014
filter_inputs_from_rel_path fix incorrect outputs resolved for filter when inputs are resolved fr… May 14, 2014
filter_multi fixed permissions on various test run.sh files May 26, 2012
filter_multi_prior_input fixed test to match behavior of new filter rule for inferring output Sep 29, 2013
filter_multiple_ext_match fix filter sometimes expecting wrong input when file extension suppli… Apr 7, 2014
filter_on_prev_input fix incorrect assertion in test Jan 11, 2014
filter_output_second_input fixed filter sometimes incorrectly refusing to allow output files that Mar 31, 2013
filter_two_same_type added test for filter with two identical filter type arguments Jan 20, 2013
filter_uses_correct_base_for_output fix filter transforms sometimes basing output file on wrong input (eg: Sep 29, 2013
filterlines many bugfixes / updates / improvements to dependency handling, output… Nov 20, 2012
folderasoutput fixed test depending on behavior of msg May 14, 2013
forward fixed another failing test due to stripping of "./" from start of paths Nov 5, 2012
forward_beats_output_same_type fix test failure due to diff 'cp -v' behavior Jun 28, 2018
forward_downstream_reference add regression test for input forwarding issue Aug 2, 2018
forward_multi fix 'forward' failing with cryptic errors when attempting to forward … Jul 19, 2014
forward_multi_inputs fix multiple inputs not forwarding correctly when referenced using "$… Dec 21, 2014
from Fixed inputs not fully restored to prior state after from {} block ex… Nov 1, 2011
from_2_matches fixed test to match slightly modified 'from' behavior when matching m… Jan 21, 2013
from_downstream_in_parallel fix input not resolved by from / input ext when reference embedded in… Jul 24, 2013
from_filter_chain experimental chaining of from and filter / transform Mar 1, 2013
from_list fix multi not actually parallelizing properly in some cases Jan 9, 2013
from_multiple_types fixed test depending on behavior of msg May 14, 2013
from_plus_prior_input fixed files failing to get cleaned up if same file was previously cle… Mar 26, 2013
from_transform_to regression test for output file name when transform inside from May 19, 2015
from_with_filter_different_input fix "from" causing original inputs not to be queried for files instea… Feb 28, 2013
from_with_output_func exec permission Mar 10, 2014
glob cleanup additoinal files May 11, 2015
huge_nested_parallel fixed deadlock when number of parallel paths exceeds configured (or d… Dec 10, 2012
huge_parallel support for controlling concurrency at the command level Dec 9, 2012
implicitmultioutput added tests for referencing $output2 outside produce/transform/filter Nov 24, 2012
innocuous_output_dir_ref fix innocuous reference to output.dir causing script failure Oct 4, 2015
input_double_ext_matching_output fix 'inputs' variable with double file extension not always resolving… Sep 12, 2014
input_ext_with_number fix test to work with slightly modified behavior regarding which inpu… May 17, 2013
inputext_ext_overlap fix test failing incorrectly Mar 10, 2014
inputextmulti prevent printout when trying to cleanup files that are not there Jan 27, 2013
inputextmulti2 fixed test depending on behavior of msg May 14, 2013
intermediate support for @intermediate and @accompanies (experimental) annotations Mar 24, 2013
large_number_files added test for processing very large number of files Apr 21, 2015
load Issue 36: Support "include" statement Jul 13, 2012
load_in_stage added test for per-branch loading of pipeline stage definitions overr… Mar 28, 2015
load_relative_to_pipeline_file_dir better formatted error message when a problem occurs in the script Jan 7, 2014
manual_resolve support for input.probe(... ending ... ) in pipeline stages to allow … Jan 15, 2016
maxmem added various tests Mar 10, 2014
memory_variable support for inline memory variable which throttls based on memory limit Aug 26, 2017
mid_pipeline_split add missing run.sh for test Nov 14, 2013
middle_parallel_no_inputs fix middle parallel section causing spurious error if no inputs provided Oct 30, 2013
multi Added 'multi' command to make it easier to run several commands in pa… Dec 23, 2012
multi_computed deleted tmp file accidentally checked in Nov 9, 2013
multi_deps fixed test depending on behavior of msg May 14, 2013
multi_input_split fixed test depending on behavior of msg May 14, 2013
multi_output_multi_exts fix single ext then overlapping dble ext causing null output Jul 13, 2018
multiplesplitgroups fixed test depending on behavior of msg May 14, 2013
nested_parallel made test check outputs more in depth since correct files were being Jun 27, 2013
nested_parallel_low_concur test for running high concurrency pipeline at low concurrency May 19, 2015
ordered_input_to_parallel fix inputs passed in wrong order to parallel stage after 'produce' wh… Aug 28, 2014
outdir_with_following_input prevent output showing in test Mar 11, 2014
output_branch_report fix possible conflicting output names on multiple branches when neste… Apr 5, 2014
output_directly_as_string support for multiple split characters in input matching patterns Mar 9, 2013
output_double_ext support for multiple file extensions when using $output variable ($ou… May 21, 2014
output_ext_multi_outputs fix problems when multiple implicit outputs computed from same input … Nov 13, 2013
output_ext_override_filter fix output extension causing wrong / confusing behavior when incombin… Feb 5, 2013
output_ext_with_number add missing run.sh for test Nov 14, 2013
output_from_prior_nested_stage fixed later stages not resolving inputs from non-final stages in prio… Mar 17, 2013
output_func added various tests Mar 10, 2014
output_in_check Fix output referenced inside check causing check to be skipped / beha… Sep 3, 2014
output_input_not_same fix transform producing same output as input when output file of same Jul 3, 2013
output_with_index_ext_and_produce fix cleanup not removing directory Apr 20, 2013
outputdir_exttx fix output.dir not working if transform annotation used Nov 29, 2013
outputext fix test incorrectly testing dependencies Sep 13, 2014
outputext2 fixed null pointer exception when output extension used but no inputs… Aug 6, 2012
outputextsame fixed test to not depend on behavior of msg May 14, 2013
outputfolder removed accidentally checked in files Nov 15, 2011
outputfolder_in_stage fix (again) test failing due to incorrect verification Sep 15, 2013
outputs_from_diff_parallel_stages fix test reporting as failing even though actually passes Aug 11, 2013
overlapping_double_ext fix exc if dbl inp ext overlaps output with sng ext Dec 16, 2017
paired_end fixed order of output from "glob" depending on the vagaries of the fi… Jan 21, 2013
parallel adjusted test to allow for variation in input used for end stage Mar 17, 2013
parallel_input_ext_original_inputs removed bogus comment from test Mar 31, 2013
parallel_only Issue 60: Pipeline consisting of ONLY parallel segment fails Aug 24, 2012
parallel_parallel added debug output to test Mar 17, 2013
parallel_prioritise_outputs_over_next fix incorrect input after parallel section with a branch having no ou… Jun 27, 2018
parallel_same_stage_outputs fixed test depending on behavior of msg May 14, 2013
parallel_start added test for case of parallel start followed by plus and more stages Oct 30, 2013
param fixed test to work with new msg behavior May 14, 2013
param_chr_override fix test missing -L flag Nov 20, 2013
param_nested_parallel fixed test depending on behavior of msg May 14, 2013
params_from_file Support for reading parameters from a file by prefixing param name with Sep 4, 2014
parent_branch_variable fix parent branches not visible in children via branch property Feb 23, 2015
per_chromosome_pure_input_output_ext finished test for fix from prior checkin May 15, 2013
per_generic_list support for arbitrary list for parallelization (experimental) Nov 20, 2013
perchromosome fixed filterInputs still not working right with chr() - behavior now Apr 2, 2013
perchromosome_filterinputs fix test failure due to altered output Aug 6, 2017
persample add run permissions May 11, 2015
persample2 deleted swap file accidentally checked in Nov 14, 2011
persample_inputotherdir Issue 63: Input files from outside working directory incorrectly redi… Aug 28, 2012
persamplefrom attempted fix for persamplefrom tests having seemingly weird concurre… Dec 9, 2012
persampleinputext fix test relying on prior broken behavior May 17, 2013
persamplenofiles fixed test failing due to updated messaging Aug 5, 2012
persampletransform fix incorrect message from check Jul 18, 2013
pipeline_require fix to not check for report generation Aug 30, 2014
preallocate set default config to not be persistent May 12, 2017
prechrinput Support for parallelizing by chromosome on existing files already spl… Dec 2, 2012
prefix fixed test breaking when behaviour was actually correct Feb 28, 2013
preserve_multi support for multiple "preserve" patterns Apr 19, 2014
produce Add Produce annotation + test Jul 18, 2012
produce_and_numbered_double_ext fix output resolved as input for produce+double ext + numbered input May 28, 2016
produce_and_output_function added regression test for bug (not yet resolved) Sep 7, 2014
produce_and_output_function_no_output_ref fix command not running when explicitly specified by produce() if ano… Sep 12, 2014
produce_existing fixed problems with circular dependencies when two pipeline stages de… Dec 6, 2012
produce_glob fixed test depending on "msg" and "Skipping" messages May 14, 2013
produce_glob_outputdir remove output file incorrectly checked in May 11, 2015
produce_glob_regex fix command not running when explicitly specified by produce() if ano… Sep 12, 2014
produce_multi added test from long ago that should have been checked in Dec 14, 2012
produce_not_found_as_input Fix transform ... to followed by double output variable extensions (.… Aug 8, 2015
produce_one_dir_one_not Fix default output directory not applied to second produce argument i… Sep 18, 2014
produce_out_of_date_inferred_inputs Merge branch 'master' of https://code.google.com/p/bpipe May 15, 2013
produce_override_output_dir add executable permission Feb 23, 2014
produce_to_dir_no_output_ref produce_to_dir_no_output_ref/hello*.txt Sep 18, 2014
produce_twodoubleext fix wrong output referenced for double ext in produce Jul 10, 2016
produce_wildcard_with_explicit_outputdir fix test returning failed status even when it succeeds (due to grep) Sep 26, 2013
produce_wildcard_with_set_outputdir added various tests Mar 10, 2014
query_with_outputdir "bpipe query" not working on files in non-default output directories Jan 11, 2014
ref_local_in_external execute mode for test Nov 29, 2013
reference_loaded_before_run test for reference to loaded variables in global scope Mar 28, 2015
region_as_bed support passing regions into Bpipe as BED file Feb 6, 2017
remake test of remake function Dec 10, 2016
replace_segment fix bad test failing incorrectly Jul 16, 2016
require_with_using add exec permission to test Mar 8, 2014
resource_limit fix custom resources not enforced when provided as map Jan 24, 2014
rscript rscript: Fix failing test May 30, 2017
segment Issue 32: Forward not working inside Transform / Filter / Produce Jun 1, 2012
segment_lib_after_load fix stages not found when defined in bpipe lib folder and referenced … Apr 21, 2015
send_to_file fix parameters passed in by command line not resolvable in templates Feb 21, 2014
set_branch_name Fix transform ... to followed by double output variable extensions (.… Aug 8, 2015
sge Issue #217: SGE executor failing with exception Jun 8, 2017
simple Fixed tests Oct 31, 2011
simpleinputoutput more progress towards transitive dependencies : cleanup implemented, … Nov 8, 2012
single_input_with_number added test for regression on input1 variable Mar 29, 2013
slow stopped log files from invocations that aren't runs from being recorded Feb 21, 2012
split_2chars remove accidentally committed file Oct 14, 2013
split_on_2_file_types switched names of output files becuase test failing? Dec 16, 2012
split_on_map_in_branch fix method missing error when multiplying by map by list Feb 20, 2015
split_outputdir enabled matching of directory name in split pattern when directory pr… Jul 7, 2014
split_regex_pattern - support for using explicit regex pattern to split files to parallel Jan 30, 2014
split_regions very basic test for region splitting Jul 15, 2016
status_command fix status command, add regression test Oct 6, 2017
succeed Ability to explicitly cause a branch to either fail or succeed premat… Jan 17, 2014
thread_division Better / fairer scheduling for dynamically allocated $thread variables Jul 17, 2015
thread_variable fixed commands executed via "multi" being allocated wrong number of Jan 16, 2016
torque_procs fix dynamic threads not used through if procs unset Aug 6, 2017
transform tidied up test Sep 12, 2013
transform_multi fixed test with incorrect checks May 26, 2012
transform_multiple_ext_match transform should be able to match whole file name, fix incorrect inpu… Apr 3, 2014
transform_one_to_one_multi fix transform(x) to(y) failing if multiple inps match x May 22, 2016
transform_one_to_two added support to transform a single file pattern to multiple targets Jan 15, 2014
transform_to fix test to conform to new transform behavior May 29, 2016
transform_to_double_ext Fix transform ... to followed by double output variable extensions (.… Aug 8, 2015
two_inputs_double_ext fix double file extension on input not resolving second and later input Feb 22, 2016
using_and_not_using fix: pipeline fails if pipeline stage is referenced both with and wit… Aug 2, 2014
using_override_global fix variable specified with 'using' not overriding global value Oct 4, 2015
using_with_default fix test failing incorrectly due to bad message text Mar 7, 2014
using_with_dynamic_load fix 'using' broken if load inside pipeline stage Feb 6, 2017
whole_input_is_extension fix files in subdirectory not resolved when whole file name matches i… Oct 5, 2015
withconfig adjust regression test check to match new output Apr 27, 2017
clean.sh Added test and fixed many issues with cleanup function Nov 13, 2012
run.sh tests/run.sh: Only choose tests from dirs that begin with alpha char May 30, 2017
testsupport.sh remove debug printout Aug 30, 2014