add salmon for counting - #36

workflow/rules/salmon_quant.rules

+#########################################################################
+# RNAflow: an automated pipeline to analyse transcriptomic data         #
+#                                                                       #
+# Authors: Rachel Legendre                                              #
+# Copyright (c) 2021-2022  Institut Pasteur (Paris).                    #
+#                                                                       #
+# This file is part of RNAflow workflow.                                #
+#                                                                       #
+# RNAflow 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.                                   #
+#                                                                       #
+# RNAflow 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 RNAflow (LICENSE).                                         #
+# If not, see <https://www.gnu.org/licenses/>.                          #
+#########################################################################
+
+
+
+rule salmon_quant:
+    input:
+       transcript = salmon_quant_transcript,
+       bam = salmon_quant_bam
+    output:
+        directory(salmon_quant_output_dir)
+    params:
+        options = salmon_quant_options,
+        libtype = config['salmon']['libtype']
+    singularity:
+        "rnaflow.img"
+    log:
+        err = salmon_quant_log_err,
+        out = salmon_quant_log_out
+    threads:
+        config['salmon']['threads']
+    envmodules:
+        "salmon/1.9.0"
+    shell:
+        """
+        salmon quant --threads {threads} --alignments {input.bam} --targets {input.transcript} --libType {params.libtype} --output {output} > {log.out} 2> {log.err}
+        """