The samples cannot be separated in the result file

[zhongzheng1999]

Hi, I am attempting to use the looper runp --looper-config examples/test_project/looper_test_refgenie.yaml functionality, but I encountered an error:

"FileNotFoundError: [Errno 2] No such file or directory: '/home/u2204084007/biosoft/pepatac-0.11.2/processed/results_pipeline/test1/stats.yaml'."

I have confirmed that I've configured the looper-config based on the examples you provided earlier. I have also uploaded the corresponding file. looper_test_refgenie.yam:

name: test_project pep_config: /home/u2204084007/biosoft/pepatac-0.11.2/examples/test_project/test_config_project_config.yaml

output_dir: "/home/u2204084007/biosoft/pepatac-0.11.2/processed/" pipeline_interfaces: sample: ["/home/u2204084007/biosoft/pepatac-0.11.2/sample_pipeline_interface.yaml"] project: ["/home/u2204084007/biosoft/pepatac-0.11.2/project_pipeline_interface.yaml"]

pipestat: results_file_path: "/home/u2204084007/biosoft/pepatac-0.11.2/processed/results_pipeline/{record_identifier}/stats.yaml"

test_config_project_config.yaml:

name: test_project pep_version: 2.0.0 sample_table: test_annotation.csv sample_modifiers: derive: attributes: [read1, read2] sources: test_data_R1: "/home/u2204084007/biosoft/pepatac-0.11.2/examples/data/{sample_name}_r1.fastq.gz" test_data_R2: "/home/u2204084007/biosoft/pepatac-0.11.2/examples/data/{sample_name}_r2.fastq.gz" imply:

• if: organism: ["human", "Homo sapiens", "Human", "Homo_sapiens"] then: genome: hg38 prealignment_names: ["rCRSd"] deduplicator: samblaster trimmer: skewer
  peak_type: fixed
  extend: "250"
  frip_ref_peaks: None

It's worth noting that in the results folder, only the "summary" folder was generated, and individual folders for each sample were not created as expected.

test_annotation.csv PEPATAC_log.txt

[donaldcampbelljr]

Hi,

You must first use looper run to generate the stats.yaml results files for the individual samples before running the project level pipelines using looper runp.

So in this case:

looper run --looper-config examples/test_project/looper_test_refgenie.yaml

then

looper runp --looper-config examples/test_project/looper_test_refgenie.yaml

Finally, you can make an html report with both the sample level and the project level results using: looper report --looper-config examples/test_project/looper_test_refgenie.yaml

[zhongzheng1999]

Later on, I encountered a new error, this time from ggplot in R, complaining about the absence of the 'linewidth' parameter. After upgrading the ggplot2 version, I was able to fix this issue. I have now obtained the complete run results. Thanks again for your assistance.