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fix: include libraries in package data #27

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merged 6 commits into from
Nov 6, 2023
Merged

fix: include libraries in package data #27

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697f076
refactor: use checkIfExists in all file() calls
kelly-sovacool Nov 6, 2023
01180e3
fix: include subdirs in assets/
kelly-sovacool Nov 6, 2023
269ffa4
chore: Merge branch 'main' into iss-26
kelly-sovacool Nov 6, 2023
2304522
docs: update changelog; bump version
kelly-sovacool Nov 6, 2023
a3776cc
fix: recurisve-include syntax for pyproject data
kelly-sovacool Nov 6, 2023
a7e5d76
chore: require setuptools 62.3 for recursive data syntax
kelly-sovacool Nov 6, 2023
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7 changes: 7 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,10 @@
## development version

### Bug fixes

- All scripts in the bin directory are now made executable for all users on biowulf (#25).
- Libraries are now copied to the assets directory (#26).

## CRUISE v0.1.0

This is the first release of CRUISE 🎉
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2 changes: 1 addition & 1 deletion VERSION
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@@ -1 +1 @@
0.1.1-dev
0.1.1-dev.1
2 changes: 1 addition & 1 deletion main.nf
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Expand Up @@ -33,7 +33,7 @@ workflow {

ch_count = params.count_table ? file(params.count_table, checkIfExists: true) : null
if (!ch_count) { // trim reads and run mageck count
TRIM_COUNT(raw_reads, file(params.library))
TRIM_COUNT(raw_reads, file(params.library, checkIfExists: true))
ch_count = TRIM_COUNT.out.count
}

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4 changes: 2 additions & 2 deletions pyproject.toml
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@@ -1,6 +1,6 @@
[build-system]
requires = [
"setuptools >= 48",
"setuptools >= 62.3.0",
"wheel >= 0.29.0",
]
build-backend = 'setuptools.build_meta'
Expand Down Expand Up @@ -61,7 +61,7 @@ Changelog = "https://github.com/CCBR/CRUISE/blob/main/docs/CHANGELOG.md"
cruise = "."

[tool.setuptools.package-data]
"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/*", "bin/*", "conf/*", "modules/*/*", "subworkflows/*/*"]
"*" = ["CITATION.cff", "LICENSE", "VERSION", "main.nf", "nextflow.config", "assets/**", "assets/**", "bin/**", "conf/**", "modules/**", "subworkflows/**"]

[tool.setuptools.dynamic]
version = {file = "VERSION"}
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2 changes: 1 addition & 1 deletion subworkflows/local/mageck.nf
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Expand Up @@ -12,7 +12,7 @@ workflow MAGECK {
TEST(count, treat, ctrl)

if (params.design_matrix) {
MLE(count, file(params.design_matrix))
MLE(count, file(params.design_matrix, checkIfExists: true))
mle_gene = MLE.out.gene
mle_sgrna = MLE.out.sgrna
} else {
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