No reports when Tower is enabled using the config file
mantczakaus opened this issue · comments
mantczakaus commented
Scenario to reproduce:
- Set up configuration file in /home_directory/.nextflow/config
singularity {
cacheDir = '/path/.nextflow/NXF_SINGULARITY_CACHEDIR'
autoMounts = true
}
conda {
cacheDir = '/path/.nextflow/NXF_CONDA_CACHEDIR'
}
process {
executor = 'slurm'
scratch = false
cleanup = false
beforeScript = 'module load singularity/3.8.6'
}
tower {
accessToken = 'XXXX'
endpoint = 'https://tower.nf/api'
enabled = true
}
- Create a folder where you’ll store the results folder, work folder and all the logs, e.g. /path/tower_tests
- Create a launch.sh in the folder you just created. This is what it should be inside of the launch.sh
#!/bin/bash
#SBATCH -N 1
#SBATCH --job-name=test
#SBATCH --mem=4G
#SBATCH --time=23:00:00
#SBATCH --cpus-per-task=2
#SBATCH --partition=work
#work on current directory (folder)
cd $SLURM_SUBMIT_DIR
#load singularity and set up memory settings to run nextflow
module load singularity/3.8.6
NXF_OPTS='-Xms1g -Xmx4g'
#run the rnaseq pipeline
nextflow run nf-core/rnaseq \
--outdir results \
-profile singularity,test \
-r 3.11.2 \
-resume
- Submit the launch.sh to the Slurm queue
sbatch launch.sh
- After the pipeline finishes running, go to Tower, find the run and go to the Reports tab
Actual results: the Reports tab is present but the reports are not displayed
Expected results: reports should be available (tower.yml present in the pipeline folder; see below)
I tested this when the pipeline was launched from the Tower (-with-tower) and the reports were there.