rnaseq: Use more memory for run_job.sh

Use newer AGAT container version
MonashBioinformaticsPlatform · Dec 4, 2024 · 1d07fd8 · 1d07fd8
1 parent dd19c6c
commit 1d07fd8
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/laxy_backend/tasks/job.py b/laxy_backend/tasks/job.py
@@ -335,7 +335,7 @@ def infer_chmod(filename, default=0o600, mappings=extension_chmod_mappings):
             with cd(working_dir):
                 with shell_env(**environment):
                     cpus = 1
-                    mem = "4G"
+                    mem = "8G"
                     time = "7-00:00:00"
                     logger.info(f"queue_type = {job.compute_resource.queue_type}")
                     if job.compute_resource.queue_type == "slurm":

diff --git a/...peline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh b/...peline_apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/3.12.0/scripts/run_job.sh
@@ -349,7 +349,7 @@ function normalize_annotations() {
     #    }
     #}
 
-    export AGAT_CONTAINER="https://depot.galaxyproject.org/singularity/agat%3A1.0.0--pl5321hdfd78af_0"
+    export AGAT_CONTAINER="https://depot.galaxyproject.org/singularity/agat%3A1.4.1--pl5321hdfd78af_0"
     if [[ ${USING_CUSTOM_REFERENCE} == "yes" && 
           $(zgrep -Pc "\texon\t.*gene_id*" "${ANNOTATION_FILE}") == 0 ]]; then
 

diff --git a/...apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh b/...apps/nf-core-rnaseq/templates/job_scripts/nf-core-rnaseq/default/input/scripts/run_job.sh
@@ -351,7 +351,7 @@ function normalize_annotations() {
     #    }
     #}
 
-    export AGAT_CONTAINER="https://depot.galaxyproject.org/singularity/agat%3A1.0.0--pl5321hdfd78af_0"
+    export AGAT_CONTAINER="https://depot.galaxyproject.org/singularity/agat%3A1.4.1--pl5321hdfd78af_0"
     if [[ ${USING_CUSTOM_REFERENCE} == "yes" && 
           $(zgrep -Pc "\texon\t.*gene_id*" "${ANNOTATION_FILE}") == 0 ]]; then