--- a/0.3.0/readme/centriflaken_hy.md	Mon Jul 25 12:57:06 2022 -0400
+++ b/0.3.0/readme/centriflaken_hy.md	Fri Jul 29 11:11:07 2022 -0400
@@ -15,7 +15,7 @@
 #### Workflow Usage
 
 ```bash
-module load cpipes/0.2.1
+module load cpipes/0.3.0
 
 cpipes --pipeline centriflaken_hy [options]
 ```
@@ -43,7 +43,7 @@
 ```text
 [Kranti.Konganti@login2-slurm ]$ cpipes --pipeline centriflaken_hy --help
 N E X T F L O W  ~  version 21.12.1-edge
-Launching `/nfs/software/apps/cpipes/0.2.1/cpipes` [wise_noyce] - revision: 72db279311
+Launching `/home/Kranti.Konganti/apps/cpipes/cpipes` [condescending_jang] - revision: 72db279311
 ================================================================================
              (o)                  
   ___  _ __   _  _ __    ___  ___ 
@@ -57,7 +57,7 @@
 --------------------------------------------------------------------------------
 Name                            : CPIPES
 Author                          : Kranti.Konganti@fda.hhs.gov
-Version                         : 0.2.1
+Version                         : 0.3.0
 Center                          : CFSAN, FDA.
 ================================================================================
 
@@ -65,7 +65,7 @@
 
 Author                          : Kranti.Konganti@fda.hhs.gov
 
-Version                         : 0.2.0
+Version                         : 0.3.0
 
 
 Usage                           : cpipes --pipeline centriflaken_hy [options]
@@ -176,6 +176,59 @@
 --centrifuge_ignore_quals       : Treat all quality values as 30 on Phred 
                                   scale. Default: false
 
+--megahit_run                   : Run MEGAHIT assembler. Default: true
+
+--megahit_min_count             : <int>. Minimum multiplicity for filtering (
+                                  k_min+1)-mers. Defaut: false
+
+--megahit_k_list                : Comma-separated list of kmer size. All 
+                                  values must be odd, in the range 15-255, 
+                                  increment should be <= 28. Ex: '21,29,39,59,
+                                  79,99,119,141'. Default: false
+
+--megahit_no_mercy              : Do not add mercy k-mers. Default: false
+
+--megahit_bubble_level          : <int>. Intensity of bubble merging (0-2), 0 
+                                  to disable. Default: false
+
+--megahit_merge_level           : <l,s>. Merge complex bubbles of length <= l*
+                                  kmer_size and similarity >= s. Default: 
+                                  false
+
+--megahit_prune_level           : <int>. Strength of low depth pruning (0-3). 
+                                  Default: false
+
+--megahit_prune_depth           : <int>. Remove unitigs with avg k-mer depth 
+                                  less than this value. Default: false
+
+--megahit_low_local_ratio       : <float>. Ratio threshold to define low 
+                                  local coverage contigs. Default: false
+
+--megahit_max_tip_len           : <int>. remove tips less than this value [<
+                                  int> * k]. Default: false
+
+--megahit_no_local              : Disable local assembly. Default: false
+
+--megahit_kmin_1pass            : Use 1pass mode to build SdBG of k_min. 
+                                  Default: false
+
+--megahit_preset                : <str>. Override a group of parameters. 
+                                  Valid values are meta-sensitive which 
+                                  enforces '--min-count 1 --k-list 21,29,39,
+                                  49,...,129,141', meta-large (large & 
+                                  complex metagenomes, like soil) which 
+                                  enforces '--k-min 27 --k-max 127 --k-step 
+                                  10'. Default: meta-sensitive
+
+--megahit_mem_flag              : <int>. SdBG builder memory mode. 0: minimum; 
+                                  1: moderate; 2: use all memory specified. 
+                                  Default: 2
+
+--megahit_min_contig_len        : <int>.  Minimum length of contigs to output. 
+                                  Default: false
+
+--spades_run                    : Run SPAdes assembler. Default: false
+
 --spades_isolate                : This flag is highly recommended for high-
                                   coverage isolate and multi-cell data. 
                                   Defaut: false
@@ -212,7 +265,7 @@
                                   Default: false
 
 --spades_only_assembler         : Runs only the SPAdes assembler module (
-                                  without read error correction).Default: 
+                                  without read error correction). Default: 
                                   false
 
 --spades_careful                : Tries to reduce the number of mismatches