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workflow/rules/adapters.rules

+#########################################################################
+# RNAsig: an automated pipeline to detect RNA signatures on viruses     #
+#                                                                       #
+# Authors: Rachel Legendre                                              #
+# Copyright (c) 2020-2021  Institut Pasteur (Paris).                    #
+#                                                                       #
+# This file is part of RNAsig workflow.                                 #
+#                                                                       #
+# RNAsig is free software: you can redistribute it and/or modify        #
+# it under the terms of the GNU General Public License as published by  #
+# the Free Software Foundation, either version 3 of the License, or     #
+# (at your option) any later version.                                   #
+#                                                                       #
+# RNAsig is distributed in the hope that it will be useful,             #
+# but WITHOUT ANY WARRANTY; without even the implied warranty of        #
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the          #
+# GNU General Public License for more details .                         #
+#                                                                       #
+# You should have received a copy of the GNU General Public License     #
+# along with RNAsig (LICENSE).                                          #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+
+rule adapters:
+    input:
+        fastq = __adapters__input_fastq
+    output:
+        __adapters__output
+    params:
+        wkdir = __adapters__wkdir,
+        options =  __adapters__options,
+        adapters = __adapters__adapt_list,
+        mode = __adapters__mode,
+	min = __adapters_min,
+	qual = __adapters_qual
+    singularity:
+        "chipuana.img"
+    threads: config['adapters']['threads'] if 'threads' in config['adapters'] else 4
+    log:
+        __adapters__log
+    shell:
+        """
+        set +o pipefail
+        
+    	tmp="{input}"
+            infiles=($tmp)
+    	
+    	tmp="{output}"
+    	outfiles=($tmp)	
+    
+    
+    	cmd="cutadapt "
+        # add mode and adapter sequences
+        cmd+=" -{params.mode} {params.adapters} -m {params.min} -q {params.qual} {params.options}  "
+        # paired end or single end
+        if [[ ${{#infiles[@]}} -eq 2 ]];
+        then
+            cmd+=" -o ${{outfiles[0]}} -p ${{outfiles[1]}}  ${{infiles[0]}} ${{infiles[1]}} "
+        else
+            cmd+=" -o ${{outfiles[0]}} ${{infiles[0]}}"
+        fi
+        #run command
+        eval "${{cmd}} > {log}"
+
+        """