# HG changeset patch
# User kkonganti
# Date 1656606874 14400
# Node ID 36ca1a1156df2621dc18cb3905e3604bd2ed165a
# Parent  d7c07f2456b459bf8f50f2a54a09a10a6d14e978
"planemo upload"

diff -r d7c07f2456b4 -r 36ca1a1156df 0.2.1/conf/modules.config
--- a/0.2.1/conf/modules.config	Wed Jun 29 23:40:53 2022 -0400
+++ b/0.2.1/conf/modules.config	Thu Jun 30 12:34:34 2022 -0400
@@ -14,7 +14,7 @@
         ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
     }
 
-    maxRetries = 21
+    maxRetries = 80
 
     withLabel: 'process_femto' {
         cpus = 2
@@ -81,7 +81,7 @@
 // Function will return after sleeping for some time. 
 // Sleep time increases exponentially by tast attempt.
 def dynamic_retry(task_retry_num, factor_by) {
-    println tas
-    sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
+    // sleep(Math.pow(2, task_retry_num.toInteger()) * factor_by.toInteger() as long)
+    sleep(Math.pow(1.27, i) as long)
     return 'retry'
-}
\ No newline at end of file
+}
diff -r d7c07f2456b4 -r 36ca1a1156df 0.2.1/nextflow.config
--- a/0.2.1/nextflow.config	Wed Jun 29 23:40:53 2022 -0400
+++ b/0.2.1/nextflow.config	Thu Jun 30 12:34:34 2022 -0400
@@ -85,7 +85,7 @@
 
     cingularitygac {
         process.executor = 'slurm'
-        executor.$slurm.exitReadTimeout = 60000
+        executor.$slurm.exitReadTimeout = 120000
         process.queue = 'q8cpu'
         process.cpus = 4
         singularity.enabled = true
@@ -110,7 +110,7 @@
 
     kondagac {
         process.executor = 'slurm'
-        executor.$slurm.exitReadTimeout = 60000
+        executor.$slurm.exitReadTimeout = 120000
         process.queue = 'q8cpu'
         process.cpus = 4
         singularity.enabled = false
diff -r d7c07f2456b4 -r 36ca1a1156df cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jun 29 23:40:53 2022 -0400
+++ b/cfsan_centriflaken.xml	Thu Jun 30 12:34:34 2022 -0400
@@ -37,6 +37,9 @@
 	--input \${pwd_path}/cpipes-input
 	--output \${pwd_path}/cpipes-output
     --fq_suffix '${fq_suffix}'
+    #if ($fq_filter_by_len > 0):
+        --fq_filter_by_len $fq_filter_by_len
+    #end if
 	--fq_filename_delim '${fq_filename_delim}'
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
@@ -67,6 +70,8 @@
             <option value="pacbio_hifi">PacBio HiFi reads (&lt;1% error)</option>
         </param>
         <param name="fq_suffix" value=".fastq.gz" type="text" label="Suffix of the R1 FASTQ or Unpaired FASTQ"/>
+        <param name="fq_filter_by_len" value="" type="integer" label="Enter minimum read length to retain before starting the analysis"
+            help="Keep this option empty to use default values. Default for centriflaken (long reads) is 4000 bp and for centriflaken_hy (short reads) is 75 bp)"/>
         <param name="fq2_suffix" value="_R2_001.fastq.gz" type="text" label="Suffix of the R2 FASTQ R2"/>
         <param name="fq_filename_delim" type="text" value="_" label="File name delimitor by which samples are grouped together (--fq_filename_delim)" 
             help="This is the delimitor by which samples are grouped together to display in the final MultiQC report. For example, if your input data sets are mango_replicate1.fastq.gz, mango_replicate2.fastq.gz, orange_replicate1_maryland.fastq.gz, orange_replicate2_maryland.fastq.gz, then to create 2 samples mango and orange, the value for --fq_filename_delim would be _ (underscore) and the value for --fq_filename_delim_idx would be 1, since you want to group by the first word (i.e. mango or orange) after splitting the filename based on _ (underscore)"/>