From cdcc42ccaaf18a89bd0a73da5de4f5b7f3a158de Mon Sep 17 00:00:00 2001 From: Donald Campbell <125581724+donaldcampbelljr@users.noreply.github.com> Date: Tue, 9 Jan 2024 10:01:54 -0500 Subject: [PATCH] add documentation clarity to rerunning pipelines https://github.com/databio/pepatac/issues/262 --- docs/faq.md | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/docs/faq.md b/docs/faq.md index 7cff73cf..d1ed7bbb 100644 --- a/docs/faq.md +++ b/docs/faq.md @@ -17,3 +17,25 @@ When deciding whether or not to merge technical replicates, you should first fol - [PCR Bottleneck Coefficient 1 (PBC1)](glossary.md#qc-output): values < 0.7 are considered concerning; values > 0.9 are ideal - [PCR Bottleneck Coefficient 2 (PBC2)](glossary.md#qc-output): values < 1.0 represent severe bottlenecking; values > 3.0 are acceptable +## What if I need to restart a run? + +There are two steps for restarting runs. When executing `looper run`, you can pass the `--ignore-flags` argument, e.g. +`looper run --looper-config /path_to_your/.looper_config.yaml --ignore-flags` +This will ignore any flags associated with the samples. Further reading: [Sample Flags](https://looper.databio.org/en/latest/faq/#why-isnt-a-sample-being-processed-by-a-pipeline-not-submitting-flag-found-_statusflag) + +If a run failed or timedout, there will be a lock on intermediate files. The pipeline interface can be modified to add the `-R` argument such that the pipeline manager (pypiper) will run in recover mode which will allow the pipeline to restart and proceed. Further reading: [Pypiper CLI: built in arguments](https://pypiper.databio.org/en/latest/cli/) + +Modify PEPATAC's sample pipeline interface, adding the `-R` argument to the command template, e.g: + +```yaml +command_template: > + {pipeline.path} + -R + --output-parent { looper.results_subdir } + --cores { compute.cores } + --mem { compute.mem } + --sample-name { sample.sample_name } + --input { sample.read1 } +``` + +