use cd-hit-est instead for nuc

tools/cd-hit/Snakefile → tools/cd-hit-est/Snakefile

 """
-CD-HIT manual
+CD-HIT-EST manual
 
 		====== CD-HIT version 4.8.1 (built on May 23 2020) ======
 
-Usage: cd-hit [Options]
+Usage: cd-hit-est [Options]
 
 Options
 
    -i	input filename in fasta format, required, can be in .gz format
+   -j	input filename in fasta/fastq format for R2 reads if input are paired end (PE) files
+ 	 -i R1.fq -j R2.fq -o output_R1 -op output_R2 or
+ 	 -i R1.fa -j R2.fa -o output_R1 -op output_R2
    -o	output filename, required
+   -op	output filename for R2 reads if input are paired end (PE) files
    -c	sequence identity threshold, default 0.9
  	this is the default cd-hit's "global sequence identity" calculated as:
  	number of identical amino acids or bases in alignment
@@ -22,9 +26,8 @@ Options
    -b	band_width of alignment, default 20
    -M	memory limit (in MB) for the program, default 800; 0 for unlimitted;
    -T	number of threads, default 1; with 0, all CPUs will be used
-   -n	word_length, default 5, see user's guide for choosing it
+   -n	word_length, default 10, see user's guide for choosing it
    -l	length of throw_away_sequences, default 10
-   -t	tolerance for redundance, default 2
    -d	length of description in .clstr file, default 20
  	if set to 0, it takes the fasta defline and stops at first space
    -s	length difference cutoff, default 0.0
@@ -57,6 +60,16 @@ Options
    -B	1 or 0, default 0, by default, sequences are stored in RAM
  	if set to 1, sequence are stored on hard drive
  	!! No longer supported !!
+   -P	input paired end (PE) reads, default 0, single file
+ 	if set to 1, please use -i R1 -j R2 to input both PE files
+   -cx	length to keep after trimming the tail of sequence, default 0, not trimming
+ 	if set to 50, the program only uses the first 50 letters of input sequence
+   -cy	length to keep after trimming the tail of R2 sequence, default 0, not trimming
+ 	if set to 50, the program only uses the first 50 letters of input R2 sequence
+ 	e.g. -cx 100 -cy 80 for paired end reads
+   -ap	alignment position constrains,  default 0, no constrain
+ 	if set to 1, the program will force sequences to align at beginings
+ 	when set to 1, the program only does +/+ alignment
    -p	1 or 0, default 0
  	if set to 1, print alignment overlap in .clstr file
    -g	1 or 0, default 0
@@ -65,12 +78,19 @@ Options
  	will cluster it into the most similar cluster that meet the threshold
  	(accurate but slow mode)
  	but either 1 or 0 won't change the representatives of final clusters
+   -r	1 or 0, default 1, by default do both +/+ & +/- alignments
+ 	if set to 0, only +/+ strand alignment
+   -mask	masking letters (e.g. -mask NX, to mask out both 'N' and 'X')
+   -match	matching score, default 2 (1 for T-U and N-N)
+   -mismatch	mismatching score, default -2
+   -gap	gap opening score, default -6
+   -gap-ext	gap extension score, default -1
+   -bak	write backup cluster file (1 or 0, default 0)
    -sc	sort clusters by size (number of sequences), default 0, output clusters by decreasing length
  	if set to 1, output clusters by decreasing size
    -sf	sort fasta/fastq by cluster size (number of sequences), default 0, no sorting
  	if set to 1, output sequences by decreasing cluster size
  	this can be very slow if the input is in .gz format
-   -bak	write backup cluster file (1 or 0, default 0)
    -h	print this help
 
    Questions, bugs, contact Weizhong Li at liwz@sdsc.edu
@@ -85,22 +105,22 @@ Options
    "CD-HIT: accelerated for clustering the next generation sequencing data", Limin Fu, Beifang Niu, Zhengwei Zhu, Sitao Wu & Weizhong Li. Bioinformatics, (2012) 28:3150-3152
 """
 
-__cd_hit_exec_command = config.get('cd_hit', {}).get('exec_command', 'cd_hit')
-__cd_hit_modules = config.get('cd_hit', {}).get('modules')
-__cd_hit_options = config.get('cd_hit', {}).get('options', '')
-__cd_hit_threads = config.get('cd_hit', {}).get('threads', 1)
+__cd_hit_est_exec_command = config.get('cd_hit_est', {}).get('exec_command', 'cd_hit_est')
+__cd_hit_est_modules = config.get('cd_hit_est', {}).get('modules')
+__cd_hit_est_options = config.get('cd_hit_est', {}).get('options', '')
+__cd_hit_est_threads = config.get('cd_hit_est', {}).get('threads', 1)
 
-rule cd_hit:
+rule cd_hit_est:
     input:
-        __cd_hit_input
+        __cd_hit_est_input
     output:
-        __cd_hit_output
+        __cd_hit_est_output
     params:
-        exec_command = __cd_hit_exec_command,
-        modules = __cd_hit_modules,
-        options = __cd_hit_options
+        exec_command = __cd_hit_est_exec_command,
+        modules = __cd_hit_est_modules,
+        options = __cd_hit_est_options
     threads:
-        __cd_hit_threads
+        __cd_hit_est_threads
     run:
         command = []
         if params.modules:

tools/cd-hit/example_usage/Snakefile → tools/cd-hit-est/example_usage/Snakefile

 configfile: "config.yaml"
 
 # ==== Snakefile path ====
-__cd-hit_rules = config.get("snakefiles", {}).get("cd_hit")
+__cd-hit_rules = config.get("snakefiles", {}).get("cd_hit_est")
 
 __main_output_dir = config.get('output_dir', 'output')
 

tools/cd-hit/example_usage/config.yaml → tools/cd-hit-est/example_usage/config.yaml

 snakefiles:
-    cd_hit: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
+    cd_hit_est: /pasteur/zeus/projets/p02/metasig/gitlab/snakemake/tools/cd-hit/Snakefile
 
 input_dir: /some/input/directory
 output_dir: /some/output/directory
@@ -9,7 +9,7 @@ samples:
 - test_00001
 - test_00002
 
-cd_hit:
-  exec_command: cd-hit
+cd_hit_est:
+  exec_command: cd-hit-est
   modules: blast+/2.10.0 cd-hit
   threads: 16