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# First, ignore everything | ||
* | ||
# Now, whitelist anything that's a directory | ||
!*/ | ||
# ignore test results | ||
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tests/test/* | ||
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#keep everything in data | ||
!metadata/* | ||
results_pipeline/ | ||
results_analysis | ||
resources/ | ||
pipelines/pypiper | ||
# ignore built docs | ||
doc/build/* | ||
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# And all the file types you're interested in. | ||
!*.sh | ||
!*.R | ||
!*.pl | ||
!*.py | ||
!*.c | ||
!*.md | ||
!*.sub | ||
!*readme.txt* | ||
!*README.txt* | ||
!*readme.md* | ||
!*README.md* | ||
!*.rst | ||
# generic ignore list: | ||
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!*.xlsx | ||
!*.yaml | ||
!*.tsv | ||
# 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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#make sure to track .gitignore | ||
!.gitignore | ||
# Gedit temporary files | ||
*~ | ||
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# ignore test results | ||
tests/test/* | ||
# libreoffice lock files: | ||
.~lock* |
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This is the content of test file a. |
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This is the content of test file b1. |
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This is the content of test file b2. |
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This is the content of test file b3. |
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This is the content of test file c. |
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sample_name,file,file2,dcol1,col_modifier | ||
b,src1,src1,src1,1 | ||
b,src1,src1,src1,2 | ||
b,src1,src1,src1,3 |
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testpipeline.sh: | ||
name: test_pipeline | ||
looper_args: False | ||
arguments: | ||
"--input": file | ||
resources: | ||
default: | ||
file_size: "0" | ||
cores: "8" | ||
mem: "32000" | ||
time: "2-00:00:00" | ||
partition: "longq" |
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testlib: testpipeline.sh | ||
testngs: testngs.sh |
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#!/bin/bash | ||
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echo $@ |
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#!/bin/bash | ||
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echo $@ |
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sample_name,library,file,file2,organism,nonmerged_col,data_source,dcol2 | ||
a,testlib,src3,src3,,src3,src3, | ||
b,testlib,,,,src3,src3,src1 | ||
c,testlib,src3,src3,,src3,src3, | ||
d,testngs,src2,src3,human,,src3, |