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feat: update spooker & jobby for ccbr_tools v0.4.1 #95

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Merged
kelly-sovacool merged 1 commit into from
May 19, 2025
Merged

feat: update spooker & jobby for ccbr_tools v0.4.1 #95

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
# LOGAN development version

- LOGAN now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#95, @kelly-sovacool)
- Fix fastq naming in fastp. (#73, @dnousome)
- Fix resources for qualimap bamqc. (#79, @dnousome)
- Now using the readthedocs theme for the docs website. (#84, @kelly-sovacool)
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2 changes: 1 addition & 1 deletion lib/Utils.groovy
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Expand Up @@ -8,7 +8,7 @@ class Utils {
if (spooker_in_path) {
try {
println "Running spooker"
def spooker_command = "spooker ${workflow.launchDir} ${pipeline_name} ${workflow.manifest.version}"
def spooker_command = "spooker --outdir ${workflow.launchDir} --name ${pipeline_name} --version ${workflow.manifest.version} --path ${workflow.projectDir}"
def command = spooker_command.execute()
command.consumeProcessOutput(out, err)
command.waitFor()
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -35,7 +35,7 @@ classifiers = [
]
requires-python = ">=3.10"
dependencies = [
"ccbr_tools@git+https://github.com/CCBR/Tools@v0.3",
"ccbr_tools@git+https://github.com/CCBR/Tools@v0.4",
"cffconvert >= 2.0.0",
"Click >= 8.1.3",
"pyyaml >= 6.0"
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