migrating CGATOxford/CGATPipelines#422

cgat-developers · May 31, 2018 · cca4b1e · cca4b1e
1 parent fb137b8
commit cca4b1e
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Showing 2 changed files with 21 additions and 20 deletions.
diff --git a/CGATPipelines/pipeline_readqc/pipeline.ini b/CGATPipelines/pipeline_readqc/pipeline.ini
@@ -205,24 +205,25 @@ options=
 ################################################################
 [fastq_screen]
 # only run fastq_screen if this is 1
-run=1
+run=0
 # --threads
 # --subset: subset of genome to be analysed
 options=--threads 10 --subset 100000
 ################################################################
 # fastq_screeen DATABASES
 # fastq_screen requires paths to bowtie indices for all 
-# contaminants. Put a '#' in front of organisms you are not
+# contaminants. Remove the '#' in front of organisms if you are
 # interested in or add other ones using the same format
 # database prefix is mandatory!
-database_human=/ifs/mirror/genomes/bowtie/hg19
-database_mouse=/ifs/mirror/genomes/bowtie/mm9
-database_rat=/ifs/mirror/genomes/bowtie/rn5
-database_yeast=/ifs/mirror/genomes/bowtie/sacCer3
-database_phix=/ifs/mirror/genomes/bowtie/phix
-database_bacteria1of2=/ifs/mirror/genomes/bowtie/ncbi_prokaryotes_1of2
-database_bacteria2of2=/ifs/mirror/genomes/bowtie/ncbi_prokaryotes_2of2
-database_contaminants=/ifs/mirror/genomes/bowtie/contaminant_list
+
+#database_human=/ifs/mirror/genomes/bowtie/hg19
+#database_mouse=/ifs/mirror/genomes/bowtie/mm9
+#database_rat=/ifs/mirror/genomes/bowtie/rn5
+#database_yeast=/ifs/mirror/genomes/bowtie/sacCer3
+#database_phix=/ifs/mirror/genomes/bowtie/phix
+#database_bacteria1of2=/ifs/mirror/genomes/bowtie/ncbi_prokaryotes_1of2
+#database_bacteria2of2=/ifs/mirror/genomes/bowtie/ncbi_prokaryotes_2of2
+#database_contaminants=/ifs/mirror/genomes/bowtie/contaminant_list
 
 ################################################################
 #Aspera ascp highspeed download tool

diff --git a/CGATPipelines/pipeline_readqc/pipeline.yml b/CGATPipelines/pipeline_readqc/pipeline.yml
@@ -205,24 +205,24 @@ reversecomplement:
     ################################################################
 fastq_screen:
     # only run fastq_screen if this is 1
-    run: 1
+    run: 0
     # --threads
     # --subset: subset of genome to be analysed
     options: --threads 10 --subset 100000
     ################################################################
     # fastq_screeen DATABASES
     # fastq_screen requires paths to bowtie indices for all 
-    # contaminants. Put a '#' in front of organisms you are not
+    # contaminants. Remove the '#' in front of organisms if you are
     # interested in or add other ones using the same format
     # database prefix is mandatory!
-    database_human: /ifs/mirror/genomes/bowtie/hg19
-    database_mouse: /ifs/mirror/genomes/bowtie/mm9
-    database_rat: /ifs/mirror/genomes/bowtie/rn5
-    database_yeast: /ifs/mirror/genomes/bowtie/sacCer3
-    database_phix: /ifs/mirror/genomes/bowtie/phix
-    database_bacteria1of2: /ifs/mirror/genomes/bowtie/ncbi_prokaryotes_1of2
-    database_bacteria2of2: /ifs/mirror/genomes/bowtie/ncbi_prokaryotes_2of2
-    database_contaminants: /ifs/mirror/genomes/bowtie/contaminant_list
+    #database_human: /ifs/mirror/genomes/bowtie/hg19
+    #database_mouse: /ifs/mirror/genomes/bowtie/mm9
+    #database_rat: /ifs/mirror/genomes/bowtie/rn5
+    #database_yeast: /ifs/mirror/genomes/bowtie/sacCer3
+    #database_phix: /ifs/mirror/genomes/bowtie/phix
+    #database_bacteria1of2: /ifs/mirror/genomes/bowtie/ncbi_prokaryotes_1of2
+    #database_bacteria2of2: /ifs/mirror/genomes/bowtie/ncbi_prokaryotes_2of2
+    #database_contaminants: /ifs/mirror/genomes/bowtie/contaminant_list
 
     ################################################################
     #Aspera ascp highspeed download tool