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Merge pull request #20 from databio/cfg2
Cfg2
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# ignore test results | ||
oldtests/test/* | ||
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# toy/experimental files | ||
*.pkl | ||
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# ignore eggs | ||
.eggs/ | ||
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# generic ignore list: | ||
*.lst | ||
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# Compiled source | ||
*.com | ||
*.class | ||
*.dll | ||
*.exe | ||
*.o | ||
*.so | ||
*.pyc | ||
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# Packages | ||
# it's better to unpack these files and commit the raw source | ||
# git has its own built in compression methods | ||
*.7z | ||
*.dmg | ||
*.gz | ||
*.iso | ||
*.jar | ||
*.rar | ||
*.tar | ||
*.zip | ||
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# Logs and databases | ||
*.log | ||
*.sql | ||
*.sqlite | ||
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# OS generated files | ||
.DS_Store | ||
.DS_Store? | ||
._* | ||
.Spotlight-V100 | ||
.Trashes | ||
ehthumbs.db | ||
Thumbs.db | ||
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# Gedit temporary files | ||
*~ | ||
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# libreoffice lock files: | ||
.~lock* | ||
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# Default-named test output | ||
microtest/ | ||
open_pipelines/ | ||
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# IDE-specific items | ||
.idea/ | ||
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# pytest-related | ||
.cache/ | ||
.coverage* | ||
.pytest_cache | ||
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# Reserved files for comparison | ||
*RESERVE* | ||
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doc/ | ||
build/ | ||
dist/ | ||
looper.egg-info/ | ||
loopercli.egg-info/ | ||
__pycache__/ | ||
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*ipynb_checkpoints* | ||
hello_looper-master* |
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protocol_mapping: | ||
bedbuncher: bedbuncher | ||
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pipelines: | ||
bedbuncher: | ||
name: bedbuncher | ||
path: pipelines/bedbuncher.py | ||
looper_args: True | ||
arguments: | ||
"--JSON-query-path": JSONquery_path | ||
"--bedset-name": bedset_name | ||
optional_arguments: | ||
"--bedbase-config": bbconfig_path | ||
resources: | ||
default: | ||
file_size: "0" | ||
cores: "1" | ||
mem: "12000" | ||
time: "00-18:00:00" | ||
pipeline_name: BEDBUNCHER | ||
pipeline_type: sample | ||
path: pipelines/bedbuncher.py | ||
input_schema: http://schema.databio.org/pipelines/bedbuncher.yaml | ||
command_template: > | ||
{pipeline.path} --JSON-query-path {sample.JSONquery_path} --bedset-name {sample.bedset_name} {% if sample.bedbase_config is defined %} --bedbase-config {sample.bedbase_config} {% endif %} |
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