diff --git a/CHANGELOG.md b/CHANGELOG.md index aa82f94..62d1123 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,8 @@ ## LOGAN development version -- Removed old bindpaths and fixed ` /gs10 doesn't exist` error (#107, @samarth8392) -- Increased pipeline walltime for slurm submission to 100 hours (#107, @samarth8392) -- Minor documentation updates for setup and running LOGAN (#107, @samarth8392) +- Removed old bindpaths and fixed ` /gs10 doesn't exist` error. (#107, @samarth8392) +- Increased pipeline walltime for slurm submission to 4 days (96 hours). (#107, #108, @samarth8392) +- Minor documentation updates for setup and running LOGAN. (#107, @samarth8392) ## LOGAN 0.3.2 diff --git a/assets/slurm_header_biowulf.sh b/assets/slurm_header_biowulf.sh deleted file mode 100644 index e40c800..0000000 --- a/assets/slurm_header_biowulf.sh +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env bash -#SBATCH --cpus-per-task=1 -#SBATCH --mem=1g -#SBATCH --time=100:00:00 -#SBATCH --parsable -#SBATCH -J "LOGAN" -#SBATCH --mail-type=BEGIN,END,FAIL -#SBATCH --output "log/slurm_%j.log" -#SBATCH --output "log/slurm_%j.log" - -module load ccbrpipeliner -module load nextflow -NXF_SINGULARITY_CACHEDIR=/data/CCBR_Pipeliner/SIFS diff --git a/assets/slurm_header_frce.sh b/assets/slurm_header_frce.sh deleted file mode 100644 index a55b94b..0000000 --- a/assets/slurm_header_frce.sh +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env bash -#SBATCH --cpus-per-task=1 -#SBATCH --mem=1g -#SBATCH --time=100:00:00 -#SBATCH --parsable -#SBATCH -J "LOGAN" -#SBATCH --mail-type=BEGIN,END,FAIL -#SBATCH --output "log/slurm_%j.log" -#SBATCH --output "log/slurm_%j.log" - -module load nextflow -NXF_SINGULARITY_CACHEDIR=/mnt/projects/CCBR-Pipelines/SIFs diff --git a/src/__main__.py b/src/__main__.py index fafc9e1..fa49be3 100644 --- a/src/__main__.py +++ b/src/__main__.py @@ -115,7 +115,7 @@ def cli(): def run(main_path, output, _mode, force_all, **kwargs): """ Run the workflow - + Note: you must first run `logan init --output ` to initialize the output directory. """ @@ -142,6 +142,7 @@ def run(main_path, output, _mode, force_all, **kwargs): force_all=force_all, pipeline_name="LOGAN", hpc_modules="nextflow/25", + hpc_walltime="4-00:00:00", **kwargs, ) finally: