@ -1,5 +1,9 @@
#!/usr/bin/env python
""" Provide functions to merge multiple versions.yml files. """
import platform
from textwrap import dedent
@ -7,6 +11,7 @@ import yaml
def _make_versions_html ( versions ) :
""" Generate a tabular HTML output of all versions for MultiQC. """
html = [
dedent (
""" \\
@ -45,47 +50,53 @@ def _make_versions_html(versions):
return " \\ n " . join ( html )
versions_this_module = { }
versions_this_module [ " $ {task.process} " ] = {
" python " : platform . python_version ( ) ,
" yaml " : yaml . __version__ ,
}
with open ( " $versions " ) as f :
versions_by_process = yaml . load ( f , Loader = yaml . BaseLoader ) | versions_this_module
# aggregate versions by the module name (derived from fully-qualified process name)
versions_by_module = { }
for process , process_versions in versions_by_process . items ( ) :
module = process . split ( " : " ) [ - 1 ]
try :
if versions_by_module [ module ] != process_versions :
raise AssertionError (
" We assume that software versions are the same between all modules. "
" If you see this error-message it means you discovered an edge-case "
" and should open an issue in nf-core/tools. "
)
except KeyError :
versions_by_module [ module ] = process_versions
versions_by_module [ " Workflow " ] = {
" Nextflow " : " $workflow.nextflow.version " ,
" $workflow.manifest.name " : " $workflow.manifest.version " ,
}
versions_mqc = {
" id " : " software_versions " ,
" section_name " : " $ {workflow.manifest.name} Software Versions " ,
" section_href " : " https://github.com/$ {workflow.manifest.name} " ,
" plot_type " : " html " ,
" description " : " are collected at run time from the software output. " ,
" data " : _make_versions_html ( versions_by_module ) ,
}
with open ( " software_versions.yml " , " w " ) as f :
yaml . dump ( versions_by_module , f , default_flow_style = False )
with open ( " software_versions_mqc.yml " , " w " ) as f :
yaml . dump ( versions_mqc , f , default_flow_style = False )
with open ( " versions.yml " , " w " ) as f :
yaml . dump ( versions_this_module , f , default_flow_style = False )
def main ( ) :
""" Load all version files and generate merged output. """
versions_this_module = { }
versions_this_module [ " $ {task.process} " ] = {
" python " : platform . python_version ( ) ,
" yaml " : yaml . __version__ ,
}
with open ( " $versions " ) as f :
versions_by_process = yaml . load ( f , Loader = yaml . BaseLoader ) | versions_this_module
# aggregate versions by the module name (derived from fully-qualified process name)
versions_by_module = { }
for process , process_versions in versions_by_process . items ( ) :
module = process . split ( " : " ) [ - 1 ]
try :
if versions_by_module [ module ] != process_versions :
raise AssertionError (
" We assume that software versions are the same between all modules. "
" If you see this error-message it means you discovered an edge-case "
" and should open an issue in nf-core/tools. "
)
except KeyError :
versions_by_module [ module ] = process_versions
versions_by_module [ " Workflow " ] = {
" Nextflow " : " $workflow.nextflow.version " ,
" $workflow.manifest.name " : " $workflow.manifest.version " ,
}
versions_mqc = {
" id " : " software_versions " ,
" section_name " : " $ {workflow.manifest.name} Software Versions " ,
" section_href " : " https://github.com/$ {workflow.manifest.name} " ,
" plot_type " : " html " ,
" description " : " are collected at run time from the software output. " ,
" data " : _make_versions_html ( versions_by_module ) ,
}
with open ( " software_versions.yml " , " w " ) as f :
yaml . dump ( versions_by_module , f , default_flow_style = False )
with open ( " software_versions_mqc.yml " , " w " ) as f :
yaml . dump ( versions_mqc , f , default_flow_style = False )
with open ( " versions.yml " , " w " ) as f :
yaml . dump ( versions_this_module , f , default_flow_style = False )
if __name__ == " __main__ " :
main ( )
nf-core-bot
1 year ago