Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 116:b6fcae1983cb

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planemo upload
author kkonganti
date Wed, 03 Jul 2024 10:45:24 -0400
parents a56f9d099aa5
children 77672281b19b
files 0.4.2/nextflow.config cfsan_centriflaken.xml
diffstat 2 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/0.4.2/nextflow.config	Tue Jul 02 16:53:12 2024 -0400
+++ b/0.4.2/nextflow.config	Wed Jul 03 10:45:24 2024 -0400
@@ -153,7 +153,7 @@
         process.executor = 'k8s'
         k8s.namespace = 'galaxy'
         k8s.serviceAccount = 'default'
-        k8s.maxErrorRetry = 5
+        k8s.maxErrorRetry = 3
         singularity.enabled = false
         docker.enabled = true
         params.enable_conda = false
--- a/cfsan_centriflaken.xml	Tue Jul 02 16:53:12 2024 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 03 10:45:24 2024 -0400
@@ -8,7 +8,7 @@
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
     time_stamp=\$(date +%Y-%m-%d-%s);
-    work_dir="\${pwd_path}/centriflaken_work_dir-"\${time_stamp};
+    work_dir="/galaxy/nf-work-dirs/centriflaken_work_dir-"\${time_stamp};
     mkdir -p \$work_dir || exit 1;
     #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
@@ -38,6 +38,7 @@
     #end if
 	$__tool_directory__/0.4.2/cpipes
     --pipeline $input_read_type_cond.pipeline_cond.pipeline
+    -work-dir \${work_dir}
     #if ($input_read_type_cond.pipeline_cond.pipeline == "centriflaken"):
         --fq_single_end true
         --flye_genome_size '${genome_size}'