extend time

ktmeaton · Oct 2, 2020 · 802a06b · 802a06b
1 parent d06ade5
commit 802a06b
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Showing 2 changed files with 4 additions and 2 deletions.
diff --git a/profiles/graham/config.yaml b/profiles/graham/config.yaml
@@ -16,7 +16,7 @@ log-handler-script: "workflow/scripts/slack_log.py"
 # ex. 4 cpus, 4GB each (total 16GB), on one node
 resources: [cpus=2, mem_mb=8000, load=100]
 # Default resources for a job
-default-resources: [cpus=1, mem_mb=2000, time_min=10, account="def-briang"]
+default-resources: [cpus=1, mem_mb=2000, time_min=20, account="def-briang"]
 # Maximum number of jobs to run
 jobs : "10"
 # Where to put the .snakemake directory

diff --git a/workflow/rules/alignment.smk b/workflow/rules/alignment.smk
@@ -46,7 +46,9 @@ rule eager:
     txt = os.path.join(logs_dir, "eager_{reads_origin}","{sample}.log"),
   shell:
     "cd {results_dir}/eager_{wildcards.reads_origin}; "
-    "nextflow run nf-core/eager -r {config[eager_rev]} \
+    "nextflow -C {config_dir}/eager.config \
+        run nf-core/eager -r {config[eager_rev]} \
+        --igenomes_ignore \
         -with-report {log.html} \
         --input {wildcards.sample}/metadata_{wildcards.sample}.tsv \
         --outdir {wildcards.sample} \