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Support multiple file versions #1247

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merged 44 commits into from
Sep 24, 2021
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1c927e9
Change filter to support multiple version file outputs
mahesh-panchal Aug 2, 2021
e147cc9
Add collectFile to combine different versions
mahesh-panchal Aug 2, 2021
2942f83
Change scrape versions to comma separate multiple versions
mahesh-panchal Aug 2, 2021
8266610
Update CHANGELOG.md
mahesh-panchal Aug 2, 2021
deaf0c1
black lint update
mahesh-panchal Aug 2, 2021
e3c5fe0
Software versions as YAML output
mahesh-panchal Aug 3, 2021
7a894d6
Add comment to add version for each tool
mahesh-panchal Aug 3, 2021
d9267e9
Update output
mahesh-panchal Aug 3, 2021
71d20e1
Collect YAML files together
mahesh-panchal Aug 3, 2021
221e492
Add workflow data to software versions
mahesh-panchal Aug 3, 2021
89d2918
Replace software versions tsv with yml
mahesh-panchal Aug 3, 2021
3945ee8
Update GET_SOFTWARE_VERSION channel names
mahesh-panchal Aug 3, 2021
e6bc9ff
Update nf_core/pipeline-template/modules/local/get_software_versions.nf
mahesh-panchal Aug 4, 2021
85839d3
Move sed for readability
mahesh-panchal Aug 4, 2021
e99da1e
Update nf_core/module-template/modules/main.nf
mahesh-panchal Aug 4, 2021
5ce54a4
Remove Dash from YAML
mahesh-panchal Aug 10, 2021
fd93ebb
Port changes from prototype https://github.com/nf-core/rnaseq/pull/689
mahesh-panchal Aug 12, 2021
3a10d60
Update comment
mahesh-panchal Aug 12, 2021
1a7993d
Update process output
mahesh-panchal Aug 12, 2021
d18174d
Add getProcessName to modules functions_nf lint
mahesh-panchal Aug 12, 2021
edae68b
Update file_exists lint to remove scrape_versions.py
mahesh-panchal Aug 12, 2021
8ae12e3
Remove scrape software version from files unchanged.
mahesh-panchal Aug 12, 2021
074f1c4
Fix YAML output
mahesh-panchal Aug 12, 2021
c21dabd
Update nf_core/module-template/modules/main.nf
mahesh-panchal Aug 12, 2021
70d14aa
Remove getSoftwareName function
mahesh-panchal Aug 12, 2021
1ee14e9
remove software var
mahesh-panchal Aug 12, 2021
a45c66d
Rename publish_dir directory
mahesh-panchal Aug 12, 2021
6682211
Update nf_core/module-template/modules/main.nf
mahesh-panchal Aug 12, 2021
30bbc8a
Update version.txt reference to versions.yml
mahesh-panchal Aug 12, 2021
a98588b
Update lint check for software
mahesh-panchal Aug 12, 2021
c46e219
Make publish_dirs lowercase
mahesh-panchal Aug 12, 2021
77a89e2
Revert "Make publish_dirs lowercase"
mahesh-panchal Aug 13, 2021
bd394ba
Revert "Update lint check for software"
mahesh-panchal Aug 13, 2021
610585c
Revert "Rename publish_dir directory"
mahesh-panchal Aug 13, 2021
2198376
Revert "remove software var"
mahesh-panchal Aug 13, 2021
4240459
Revert "Remove getSoftwareName function"
mahesh-panchal Aug 13, 2021
3bf1b7f
Remove def software line
mahesh-panchal Aug 13, 2021
d965d62
Remove reference to $software
mahesh-panchal Aug 13, 2021
8635612
Update output docs (software_versions.tsv ->software_versions.yml)
mahesh-panchal Sep 14, 2021
2af8709
Do not update nf-core modules in pipeline template yet
grst Sep 23, 2021
6c52385
Update functions.nf in module template and in local pipeline modules
grst Sep 23, 2021
da8dadb
Show linting messages when linting tests failed
grst Sep 23, 2021
9a0dfd9
Print linting error message
grst Sep 23, 2021
82ce4b4
Update nf_core/pipeline-template/docs/output.md
grst Sep 23, 2021
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Add getProcessName to modules functions_nf lint
mahesh-panchal committed Aug 12, 2021

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This commit was signed with the committer’s verified signature.
jrjohnson Jon Johnson
commit d18174d69a52aa5b56037a9d33e8a5e2ff314869
2 changes: 1 addition & 1 deletion nf_core/modules/lint/functions_nf.py
Original file line number Diff line number Diff line change
@@ -22,7 +22,7 @@ def functions_nf(module_lint_object, module):
return

# Test whether all required functions are present
required_functions = ["getSoftwareName", "initOptions", "getPathFromList", "saveFiles"]
required_functions = ["getSoftwareName", "getProcessName", "initOptions", "getPathFromList", "saveFiles"]
lines = "\n".join(lines)
contains_all_functions = True
for f in required_functions: