Commit e1eb78b6 authored by Gael  MILLOT's avatar Gael MILLOT
Browse files

v7.9.0 release: Pipeline improved

parent beb4ea5c
......@@ -209,6 +209,11 @@ Gitlab developers
## WHAT'S NEW IN
### v7.9.0
1) Pipeline improved
### v7.8.0
1) Pipeline improved
......
......@@ -457,7 +457,7 @@ if(ncol(obs.freq) > 0){
x.second.tick.nb = NULL,
y.top.extra.margin = 0.05,
y.bottom.extra.margin = 0,
y.lim = c(0, 10),
y.lim = c(0, 500),
y.lab = "Site number",
y.log = "no",
y.second.tick.nb = 5,
......
......@@ -1043,7 +1043,7 @@ process backup {
"""
echo -e "\\n\\n<br /><br />\\n\\n### Backup\\n\\n" > report.rmd
echo -e "See the [reports](./reports) folder for all the details of the analysis, including the parameters used in the .config file" >> report.rmd
echo -e "\\n\\n<br /><br />\\n\\nFull .nextflow.log is in: ${launchDir}<br />The one in the [reports](./reports) folder is not complete (miss the end)" >> report.rmd
echo -e "\\n\\nFull .nextflow.log is in: ${launchDir}<br />The one in the [reports](./reports) folder is not complete (miss the end)" >> report.rmd
"""
}
......@@ -1058,7 +1058,7 @@ process workflowVersion { // create a file with the workflow version in out_path
script:
"""
echo -e "\\n\\n<br /><br />\\n\\n### Workflow Version\\n\\n" > report.rmd
echo "Project (empty means no .git folder where the main.nf file is present): " \$(git -C ${projectDir} remote -v | head -n 1) >> report.rmd # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo
echo -e "\\n\\nGENERAL:\\n\\nProject (empty means no .git folder where the main.nf file is present): " \$(git -C ${projectDir} remote -v | head -n 1) >> report.rmd # works only if the main script run is located in a directory that has a .git folder, i.e., that is connected to a distant repo
echo "<br />Git info (empty means no .git folder where the main.nf file is present): " \$(git -C ${projectDir} describe --abbrev=10 --dirty --always --tags) >> report.rmd # idem. Provide the small commit number of the script and nextflow.config used in the execution
echo "<br />Cmd line: ${workflow.commandLine}" >> report.rmd
echo "<br />execution mode": ${system_exec} >> report.rmd
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment