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Error: looper requires JWT for retrieving public PEP from PEPhub

5

I entered a registry path to a public PEP in my looper config. I ran `looper run` and I get this error: ``` looper run -d -l 1 Looper version:...

nsheff

looper config should allow for pipestat pephub path.

1

Currently, working on the docs, and I realized that looper needs to be able to add the `pephub_path` key to the pipestat namespace so that this path can be passed...

donaldcampbelljr

looper cli is not taking priority if cli modifiers are used in looper config

3

if i use looper with a limit command `looper run --limit 2` but then place this in my looper config: ``` pep_config: project/project_config.yaml output_dir: "results" pipeline_interfaces: - pipeline/pipeline_interface.yaml cli: run:...

donaldcampbelljr

Looper does not overwrite pipestat config, should it?

1

Originally, looper would overwrite the pipestat config upon executing `looper run`. However, several months ago, we changed it such that it will not overwrite the pipestat config if it finds...

donaldcampbelljr

Cannot run through the Extended tutorial

2

Hi, I am trying to run the Extended tutorial. After following all the steps, I used looper to run a project-level analysis with the given command. However, I noticed that...

binbinZhao2017

Basically, here is my looper config: ``` pep_config: metadata/pep_config.yaml output_dir: ${RESULTS} pipeline_interfaces: - pipeline/pipeline_interface.yaml pipestat: pephub_path: donaldcampbelljr/human_seqcol_digests:default flag_file_dir: ${RESULTS}/flags ``` My pipeline interface: ``` pipeline_name: brickyard_refgenome_download sample_interface: command_template: > python3...

donaldcampbelljr

This works: ``` pep_config: metadata/pep_config.yaml output_dir: ${RESULTS} pipeline_interfaces: - pipeline/pipeline_interface.yaml pipestat: pephub_path: donaldcampbelljr/human_seqcol_digests:default ``` This does not work: ``` pep_config: metadata/pep_config.yaml output_dir: ${RESULTS} pipeline_interfaces: - pipeline/pipeline_interface.yaml pipestat: pephub_path: ${PEPHUB_PATH} ```

donaldcampbelljr

Error using `--sel-excl` flag: `TypeError: 'in <string>' requires string as left operand, not list`

1

I just hit an error using `looper` and the `--sel-excl` flag. I was trying to exclude a specific set of samples from running through my pipeline. As such I was...

nleroy917

`looper.write_sample_yaml` pre-submit function assumes the sample has `sample_name` as an attribute

7

I was trying to submit jobs by leveraging the `write_sample_yaml` pre-submit function. This was my `pipeline_interface.yaml`: ```yaml pipeline_name: cranger-atac pipeline_type: sample pre_submit: python_functions: - looper.write_sample_yaml command_template: > python {looper.piface_dir}/run.py {looper.output_dir}/submission/{sample.id}_sample.yaml...

nleroy917

Document subsample table and presubmission hooks

1

We had an issue where @nleroy917 wanted to use subsamples but it was difficult to figure out how to use a subsample table AND pass the subsamples to a pipeline....

donaldcampbelljr