Merge pull request #12 from HCGB-IGTP/tRNA_devel

tRNA module development

XICRA_pip/XICRA/config/software/dependencies.csv

@@ -6,12 +6,13 @@ Rscript,--version,.*version\s([0-9\.]+).*,3.5.1,Rscript
 java,,,na,java
 python,--version,([0-9\.]+),3.6,python
 perl,--version,v([0-9]\.[0-9]+\.[0-9]),5.18.1,perl
-make,--version,GNU Make ([0-9]\.[0-9].*),4.0,make
+make,--version,GNU Make ([0-9]\.[0-9].*),4,make
 git,--version,git version ([0-9]\.[0-9]+\.[0-9]),2.1.0,git
 fastqjoin,,,na,fastq-join
 sRNAbench,-h,([0-9\.]+),1.5,sRNAbench.jar
 miRTop,--version,([0-9\.]+).*,0.4.23,mirtop
 optimir,,,na,optimir
 miraligner,,,na,miraligner.jar
 STAR,--version,([0-9\.]+).*,2.6.1,STAR
-featureCounts,-v,v([0-9\.]+).*,1.5.1,featureCounts
+featureCounts,-v,v([0-9\.]+).*,1.5.1,featureCounts
+MINTmap,,,na,MINTmap

XICRA_pip/XICRA/modules/__init__.py

@@ -7,7 +7,8 @@
 	'miRNA',
 	'prep',
 	'qc',
-	'trimm'	
+	'trimm',
+	'tRNA'
 ]
 
 from XICRA.modules import *

XICRA_pip/XICRA/modules/help_XICRA.py

@@ -7,10 +7,8 @@
 Help messages for different scripts, modules
 """
 from termcolor import colored
-
 from HCGB import functions
 
-
 ###############
 def help_fastq_format():
     """
@@ -153,18 +151,27 @@ def help_fastq_format():
     print ("name_L00x_R2.fastq\tname_L00x_R2.fq\nname_L00x_R2.fastq.gz\tname_L00x_R2.fq.gz")
     print ("\n")
 
-
+###############
 def project_help():
     return ()
 
+###############
 def multiqc_help():
     return ()
 
+###############
 def print_help_adapters():
     return()
 
+###############
 def help_join_reads():
     return ()
 
+###############
 def help_miRNA():
     return ()
+
+###############
+def help_tRNA():
+    return ()
+