Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 17:1cb92deb15f8

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"planemo upload"
author kkonganti
date Tue, 28 Jun 2022 19:54:23 -0400
parents 589620eec35d
children 4f31b641f6fd
files 0.2.1/conf/modules.config 0.2.1/nextflow.config cfsan_centriflaken.xml
diffstat 3 files changed, 17 insertions(+), 17 deletions(-) [+]
line wrap: on
line diff
--- a/0.2.1/conf/modules.config	Tue Jun 28 18:18:17 2022 -0400
+++ b/0.2.1/conf/modules.config	Tue Jun 28 19:54:23 2022 -0400
@@ -17,51 +17,51 @@
     maxRetries = 11
 
     withLabel: 'process_femto' {
-        cpus= 1
+        cpus = 2
     }
 
     withLabel: 'process_pico' {
-        cpus= 2
+        cpus = 2
     }
 
     withLabel: 'process_nano' {
-        cpus= 4
+        cpus = 4
     }
 
     withLabel: 'process_micro' {
-        cpus= 8
+        cpus = 8
     }
 
     withLabel: 'process_only_mem_low' {
-        cpus= 1
+        cpus = 2
     }
 
     withLabel: 'process_only_mem_medium' {
-        cpus= 1
+        cpus = 2
     }
 
     withLabel: 'process_only_mem_high' {
-        cpus= 1
+        cpus = 2
     }
 
     withLabel: 'process_low' {
-        cpus= 10
+        cpus = 8
     }
 
     withLabel: 'process_medium' {
-        cpus= 10
+        cpus = 8
     }
 
     withLabel: 'process_high' {
-        cpus= 10
+        cpus = 8
     }
 
     withLabel: 'process_higher' {
-        cpus= 10
+        cpus = 8
     }
 
     withLabel: 'process_gigantic' {
-        cpus= 10
+        cpus = 8
     }
 }
 
--- a/0.2.1/nextflow.config	Tue Jun 28 18:18:17 2022 -0400
+++ b/0.2.1/nextflow.config	Tue Jun 28 19:54:23 2022 -0400
@@ -86,7 +86,7 @@
     cingularitygac {
         process.executor = 'slurm'
         executor.$slurm.exitReadTimeout = 60000
-        process.queue = 'q16cpu'
+        process.queue = 'q8cpu'
         process.cpus = 4
         singularity.enabled = true
         singularity.autoMounts = true
@@ -111,7 +111,7 @@
     kondagac {
         process.executor = 'slurm'
         executor.$slurm.exitReadTimeout = 60000
-        process.queue = 'q16cpu'
+        process.queue = 'q8cpu'
         process.cpus = 4
         singularity.enabled = false
         docker.enabled = false
--- a/cfsan_centriflaken.xml	Tue Jun 28 18:18:17 2022 -0400
+++ b/cfsan_centriflaken.xml	Tue Jun 28 19:54:23 2022 -0400
@@ -60,9 +60,9 @@
         </param>
     </inputs>
     <outputs>
-        <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}">
-            <discover_datasets pattern="(?P&lt;name&gt;.*)\.html" ext="html" assign_primary_output="true" directory="./cpipes-output/${pipeline}-multiqc"/>
-        </data>
+        <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="./cpipes-output/${pipeline}-multiqc/multiqc_report.html"/>
+            <!-- <discover_datasets pattern="(?P&lt;name&gt;.*)\.html" ext="html" assign_primary_output="true" directory="./cpipes-output/${pipeline}-multiqc"/> -->
+        <!-- </data> -->
         <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
             <discover_datasets pattern="(?P&lt;designation&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" visible="true" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
         </data>