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workflow/rules/bowtie2_index.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 bowtie2_index:
+    """
+    Genome indexation for Bowtie2 mapper
+
+    Required input:
+        __bowtie2_index__fasta: the reference genome to indexed in FASTA format
+
+    Required output:
+        __bowtie2_index__output_done: done file for bowtie2 mapping rule
+
+    params:
+        __bowtie2_index__output_prefix: the directory where write the index
+
+    """
+    input:
+        fasta =  __bowtie2_index__fasta
+    output:
+        __bowtie2_index__output_done
+    singularity:
+        "rnasig.img"
+    params:
+        prefix = __bowtie2_index__output_prefix
+    log:
+        __bowtie2_index__log
+    shell:
+        """
+        bowtie2-build {input.fasta} {params.prefix}  2> {log}
+        samtools faidx {input.fasta} 2>> {log}
+
+        """