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donaldcampbelljrdonaldcampbelljr
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update pipeline interfaces to use new consolidated interface for both sample and project commands pepkit/looper#493 
1 parent 860a907 commit 4a3eb8c

26 files changed

+60
-91
lines changed

‎advanced/.looper.yaml

+4-6
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@@ -1,10 +1,8 @@
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pep_config: project/project_config.yaml
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output_dir: "results"
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pipeline_interfaces:
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sample:
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- ../pipeline/pipeline_interface1_sample.yaml
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- ../pipeline/pipeline_interface2_sample.yaml
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project:
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- ../pipeline/pipeline_interface1_project.yaml
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- ../pipeline/pipeline_interface2_project.yaml
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- pipeline/pipeline_interface1_sample.yaml
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- pipeline/pipeline_interface2_sample.yaml
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- pipeline/pipeline_interface1_project.yaml
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- pipeline/pipeline_interface2_project.yaml
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‎advanced/.looper_advanced_pipestat.yaml

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@@ -1,9 +1,8 @@
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pep_config: project/project_config.yaml
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output_dir: "results"
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pipeline_interfaces:
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sample:
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- ../pipeline/pipestat_pipeline_interface1_sample.yaml
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- ../pipeline/pipestat_pipeline_interface2_sample.yaml
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- pipeline/pipestat_pipeline_interface1_sample.yaml
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- pipeline/pipestat_pipeline_interface2_sample.yaml
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pipestat:
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results_file_path: results.yaml
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flag_file_dir: results/flags

‎advanced/pipeline/pipeline_interface1_project.yaml

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@@ -1,9 +1,9 @@
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pipeline_name: PIPELINE1
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pipeline_type: project
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output_schema: output_schema.yaml
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var_templates:
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path: "{looper.piface_dir}/col_pipeline1.py"
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command_template: >
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python3 {pipeline.var_templates.path} --project-name {project.name}
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project_interface:
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command_template: >
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python3 {pipeline.var_templates.path} --project-name {project.name}
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‎advanced/pipeline/pipeline_interface1_sample.yaml

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@@ -1,13 +1,13 @@
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pipeline_name: PIPELINE1
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pipeline_type: sample
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input_schema: https://schema.databio.org/pep/2.0.0.yaml
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output_schema: output_schema.yaml
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var_templates:
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path: "{looper.piface_dir}/pipeline1.py"
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pre_submit:
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python_functions:
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- looper.write_sample_yaml
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command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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sample_interface:
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command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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‎advanced/pipeline/pipeline_interface2_project.yaml

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@@ -1,10 +1,10 @@
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pipeline_name: OTHER_PIPELINE2
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pipeline_type: project
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output_schema: output_schema.yaml
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var_templates:
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path: "{looper.piface_dir}/col_pipeline2.py"
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command_template: >
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python3 {pipeline.var_templates.path} --project-name {project.name}
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project_interface:
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command_template: >
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python3 {pipeline.var_templates.path} --project-name {project.name}
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compute:
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size_dependent_variables: resources-project.tsv
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‎advanced/pipeline/pipeline_interface2_sample.yaml

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@@ -1,13 +1,13 @@
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pipeline_name: OTHER_PIPELINE2
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pipeline_type: sample
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output_schema: output_schema.yaml
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var_templates:
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path: "{looper.piface_dir}/other_pipeline2.py"
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pre_submit:
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python_functions:
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- looper.write_sample_yaml
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command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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sample_interface:
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command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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compute:
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size_dependent_variables: resources-sample.tsv
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‎advanced/pipeline/pipestat_pipeline_interface1_sample.yaml

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@@ -1,13 +1,13 @@
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pipeline_name: example_pipestat_pipeline
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pipeline_type: sample
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input_schema: https://schema.databio.org/pep/2.0.0.yaml
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output_schema: pipestat_output_schema.yaml
54
var_templates:
65
path: "{looper.piface_dir}/pipeline1.py"
76
pre_submit:
87
python_functions:
98
- looper.write_sample_yaml
10-
command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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sample_interface:
10+
command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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1313

‎advanced/pipeline/pipestat_pipeline_interface2_sample.yaml

+3-3
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@@ -1,14 +1,14 @@
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pipeline_name: example_pipestat_pipeline
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pipeline_type: sample
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input_schema: https://schema.databio.org/pep/2.0.0.yaml
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output_schema: pipestat_output_schema.yaml
54
var_templates:
65
path: "{looper.piface_dir}/other_pipeline2.py"
76
pre_submit:
87
python_functions:
98
- looper.write_sample_yaml
10-
command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
9+
sample_interface:
10+
command_template: >
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python3 {pipeline.var_templates.path} --sample-name {sample.sample_name} --req-attr {sample.attr}
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compute:
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size_dependent_variables: resources-sample.tsv
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‎csv/.looper.yaml

+1-1
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@@ -2,4 +2,4 @@ pep_config: project/sample_annotation.csv # local path to CSV
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# pep_config: pepkit/hello_looper:default # you can also use a pephub registry path
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output_dir: "results"
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pipeline_interfaces:
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sample: pipeline/pipeline_interface.yaml
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- pipeline/pipeline_interface.yaml

‎csv/pipeline/pipeline_interface.yaml

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@@ -2,5 +2,9 @@ pipeline_name: count_lines
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pipeline_type: sample
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var_templates:
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pipeline: '{looper.piface_dir}/count_lines.sh'
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command_template: >
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{pipeline.var_templates.pipeline} {sample.file}
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sample_interface:
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command_template: >
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{pipeline.var_templates.pipeline} {sample.file}
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project_interface:
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command_template: >
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{pipeline.var_templates.pipeline} "data/*.txt"

‎csv/pipeline/pipeline_interface_project.yaml

-6
This file was deleted.

‎intermediate/.looper.yaml

+1-1
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@@ -2,4 +2,4 @@ pep_config: project/project_config.yaml # local path to pep config
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# pep_config: pepkit/hello_looper:default # you can also use a pephub registry path
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output_dir: "results"
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pipeline_interfaces:
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sample: pipeline/pipeline_interface.yaml
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- pipeline/pipeline_interface.yaml

‎intermediate/.looper_project.yaml

-4
This file was deleted.

‎intermediate/pipeline/pipeline_interface.yaml

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@@ -1,6 +1,9 @@
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pipeline_name: count_lines
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pipeline_type: sample
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var_templates:
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pipeline: '{looper.piface_dir}/count_lines.sh'
5-
command_template: >
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{pipeline.var_templates.pipeline} {sample.file}
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sample_interface:
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command_template: >
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{pipeline.var_templates.pipeline} {sample.file}
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project_interface:
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command_template: >
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{pipeline.var_templates.pipeline} "data/*.txt"

‎intermediate/pipeline/pipeline_interface_bulker.yaml

-11
This file was deleted.

‎intermediate/pipeline/pipeline_interface_project.yaml

-6
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‎minimal/.looper.yaml

+1-1
Original file line numberDiff line numberDiff line change
@@ -2,4 +2,4 @@ pep_config: project/project_config.yaml # local path to pep config
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# pep_config: pepkit/hello_looper:default # you can also use a pephub registry path
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output_dir: "results"
44
pipeline_interfaces:
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sample: pipeline/pipeline_interface.yaml
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- pipeline/pipeline_interface.yaml

‎minimal/pipeline/pipeline_interface.yaml

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@@ -1,6 +1,6 @@
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pipeline_name: count_lines
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pipeline_type: sample
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var_templates:
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pipeline: '{looper.piface_dir}/count_lines.sh'
5-
command_template: >
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{pipeline.var_templates.pipeline} {sample.file}
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sample_interface:
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command_template: >
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{pipeline.var_templates.pipeline} {sample.file}

‎pephub/.looper.yaml

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@@ -1,4 +1,4 @@
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pep_config: pepkit/hello_looper:default # pephub registry path or local path
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output_dir: results
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pipeline_interfaces:
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sample: pipeline/pipeline_interface.yaml
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- pipeline/pipeline_interface.yaml

‎pephub/pipeline/pipeline_interface.yaml

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@@ -2,5 +2,9 @@ pipeline_name: count_lines
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pipeline_type: sample
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var_templates:
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pipeline: '{looper.piface_dir}/count_lines.sh'
5-
command_template: >
6-
{pipeline.var_templates.pipeline} {sample.file}
5+
sample_interface:
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command_template: >
7+
{pipeline.var_templates.pipeline} {sample.file}
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project_interface:
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command_template: >
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{pipeline.var_templates.pipeline} "data/*.txt"

‎pephub/pipeline/pipeline_interface_project.yaml

-6
This file was deleted.

‎pipestat/.looper.yaml

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@@ -1,8 +1,7 @@
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pep_config: ./project/project_config.yaml # pephub registry path or local path
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output_dir: ./results
33
pipeline_interfaces:
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sample: ./pipeline_pipestat/pipeline_interface.yaml
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project: ./pipeline_pipestat/pipeline_interface_project.yaml
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- pipeline_pipestat/pipeline_interface.yaml
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pipestat:
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results_file_path: results.yaml
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flag_file_dir: results/flags

‎pipestat/.looper_pipestat_shell.yaml

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@@ -1,7 +1,7 @@
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pep_config: ./project/project_config.yaml # pephub registry path or local path
22
output_dir: ./results
33
pipeline_interfaces:
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sample: ./pipeline_pipestat/pipeline_interface_shell.yaml
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- pipeline_pipestat/pipeline_interface_shell.yaml
55
pipestat:
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results_file_path: results.yaml
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flag_file_dir: results/flags

‎pipestat/pipeline_pipestat/pipeline_interface.yaml

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@@ -1,5 +1,8 @@
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pipeline_name: example_pipestat_pipeline
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pipeline_type: sample
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output_schema: pipestat_output_schema.yaml
4-
command_template: >
5-
python3 {looper.piface_dir}/count_lines.py {sample.file} {sample.sample_name} {pipestat.results_file} {pipestat.output_schema}
3+
sample_interface:
4+
command_template: >
5+
python3 {looper.piface_dir}/count_lines.py {sample.file} {sample.sample_name} {pipestat.results_file} {pipestat.output_schema}
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project_interface:
7+
command_template: >
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{pipeline.var_templates.pipeline} "data/*.txt"

‎pipestat/pipeline_pipestat/pipeline_interface_project.yaml

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‎pipestat/pipeline_pipestat/pipeline_interface_shell.yaml

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pipeline_name: example_pipestat_pipeline
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pipeline_type: sample
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output_schema: pipestat_output_schema.yaml
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command_template: >
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{looper.piface_dir}/count_lines_pipestat.sh {sample.file} {sample.sample_name} {pipestat.config_file}
3+
sample_interface:
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command_template: >
5+
{looper.piface_dir}/count_lines_pipestat.sh {sample.file} {sample.sample_name} {pipestat.config_file}

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