2) Create a folder where you’ll store the results folder, work folder and all the logs, e.g. /path/tower_tests
3) 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
4) Submit the launch.sh to the Slurm queue
sbatch launch.sh
5) 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.
Scenario to reproduce: 1) Set up configuration file in /home_directory/.nextflow/config
2) Create a folder where you’ll store the results folder, work folder and all the logs, e.g. /path/tower_tests 3) Create a launch.sh in the folder you just created. This is what it should be inside of the launch.sh
4) Submit the launch.sh to the Slurm queue
sbatch launch.sh
5) After the pipeline finishes running, go to Tower, find the run and go to the Reports tabActual 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)