# HG changeset patch
# User kkonganti
# Date 1656521102 14400
# Node ID b9cd7722d51b2afe950f2199ce01739c33c1ef75
# Parent  05b6b4edfd58e9ebc0e7369ca440396ad727e72e
"planemo upload"

diff -r 05b6b4edfd58 -r b9cd7722d51b 0.2.1/conf/modules.config
--- a/0.2.1/conf/modules.config	Wed Jun 29 09:47:38 2022 -0400
+++ b/0.2.1/conf/modules.config	Wed Jun 29 12:45:02 2022 -0400
@@ -11,10 +11,10 @@
     ]
 
     errorStrategy = {
-        ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 1000) : 'finish'
+        ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
     }
 
-    maxRetries = 11
+    maxRetries = 21
 
     withLabel: 'process_femto' {
         cpus = 2
diff -r 05b6b4edfd58 -r b9cd7722d51b cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jun 29 09:47:38 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jun 29 12:45:02 2022 -0400
@@ -30,6 +30,17 @@
 	--fq_filename_delim_idx $fq_filename_delim_idx
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
 	--flye_genome_size '${genome_size}'
+    #if ($long_read_platform == "nanopore_corr"):
+        --flye_nano_corr true --flye_nano_raw false
+    #elif ($long_read_platform == "nanopore_hq"):
+        --flye_nano_hq true --flye_nano_raw false
+    #elif ($long_read_platform == "pacbio_raw"):
+        --flye_pacbio_raw true --flye_nano_raw false
+    #elif ($long_read_platform == "pacbio_corr"):
+        --flye_pacbio_corr true --flye_nano_raw false
+    #elif ($long_read_platform == "pacbio_hifi"):
+        --flye_pacbio_hifi true --flye_nano_raw false
+    #end if
 	-profile $runtime_profile
     -resume;
     mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
@@ -47,6 +58,15 @@
             <option value="single">Single-End</option>
             <option value="paired">Paired-End</option>
         </param>
+        <param name="long_read_platform" type="select" label="Mention long read sequencing platform and type" value="nanopore_raw"
+            help="THIS OPTION IS IGNORED IF THE INPUT READS ARE SHORT READS.">
+            <option value="nanopore_raw">Nanopore raw reads, pre-Guppy5 (&lt;20% error)</option>
+            <option value="nanopore_corr">Nanopore reads that were corrected with other methods (&lt;3% error)</option>
+            <option value="nanopore_hq">Nanopore high-quality reads, Guppy5+ SUP or Q20 (5% error)</option>
+            <option value="pacbio_raw">PacBio regular CLR reads (&lt;20% error)</option>
+            <option value="pacbio_corr">PacBio reads that were corrected with other methods (&lt;3% error)</option>
+            <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="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)"