Nextflow outputs
Nextflow creates 2 main output directories: results and work in the current directory.
You can change the working directory with the -work-dir option.
$ ls -la
drwxr-xr-x 3 bleuet BIOINFO 4096 23 dec. 12:11 .nextflow => internal files
-rw-r--r-- 1 bleuet BIOINFO 108 23 dec. 12:07 nextflow.config => config file
-rw-r--r-- 1 bleuet BIOINFO 10962 23 dec. 12:11 .nextflow.log => log file with all intermediate directories
drwxr-xr-x 2 bleuet BIOINFO 4096 23 dec. 12:11 results => final results
drwxr-xr-x 8 bleuet BIOINFO 4096 23 dec. 12:10 work => working and temporary files
results directory
Depending on the executed workflow the results files will be organized differently in results directory.
work directory
Each job execution has a sub-directory. If a job fails, you can go into the directory and check the executed command. We can have a look to the directory corresponding to the failed job and have access to the log and command file.
$ ls -la work/40/944143ebbcc45aa0e4bf2f8ba9dab6/
total 4
drwxr-xr-x 3 cnoirot BIOINFO 4096 24 mars 10:00 ..
-rw-r--r-- 1 cnoirot BIOINFO 2514 24 mars 10:00 .command.run
-rw-r--r-- 1 cnoirot BIOINFO 36 24 mars 10:00 .command.sh => the command to execute
-rw-r--r-- 1 cnoirot BIOINFO 0 24 mars 10:00 .command.begin
-rw-r--r-- 1 cnoirot BIOINFO 0 24 mars 10:00 .command.err => error file
-rw-r--r-- 1 cnoirot BIOINFO 13 24 mars 10:00 .command.log
-rw-r--r-- 1 cnoirot BIOINFO 13 24 mars 10:00 .command.out => output file
drwxr-xr-x 2 cnoirot BIOINFO 4096 24 mars 10:00 .
-rw-r--r-- 1 cnoirot BIOINFO 1 24 mars 10:00 .exitcode
See the log file to get the execution error .command.log.
The executed command is in file .command.sh. In case of error, to
re-execute the command in same environment as during nextflow execution,
you should execute with the singularity image. Details of this step is
available in singularity page
Exercise 3 :
- Go into a work directory of a job previously executed by workflow hello.
- Print content of all files
.command.sh.command.log.command.out.command.log