add minimap2

config/config.yaml

@@ -116,6 +116,7 @@ adapters:
 #
 # :Parameters:
 #
+# - do: if unchecked, this rule is ignored
 # - options: any options recognised by bowtie2 tool
 # - threads: number of threads to be used
 #===============================================================================
@@ -131,6 +132,7 @@ bowtie2_mapping:
 #
 # :Parameters:
 #
+# - do: if unchecked, this rule is ignored
 # - options: any options recognised by bowtie2 tool
 # - threads: number of threads to be used
 #===============================================================================
@@ -142,11 +144,29 @@ star_mapping:
     options: "--outFilterMismatchNoverLmax 0.05 --outSAMunmapped Within --sjdbOverhang 250"
     threads: 4
 
+
+#===============================================================================
+# Mapping with minimap2
+#
+# :Parameters:
+#
+# - do: if unchecked, this rule is ignored 
+# - options: any options recognised by minimap2 tool
+# - threads: number of threads to be used
+#===============================================================================
+
+
+minimap2:
+    do: yes
+    options: "-ax sr"
+    threads: 4
+
 #===============================================================================
 # pseudo mapping with kallisto
 #
 # :Parameters:
 #
+# - do: if unchecked, this rule is ignored
 # - fasta: Fasta file for the kallisto index to be used for quantification
 # - gtf: GTF file for transcriptome information (required for --genomebam)
 # - kmer: k-mer (odd) length (default: 31, max value: 31)
@@ -189,12 +209,14 @@ feature_counts:
 #
 # - do: if unchecked, this rule is ignored
 # - options: options related to deeptools
-# see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
-# for more information about effective Genome Size
+#   see https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html
+#       for more information about effective Genome Size
+# - threads: number of threads to be used
 
 bamCoverage:
     do: yes
-    options: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 " 
+    options: "--filterRNAstrand forward --effectiveGenomeSize 120000 " 
+    options_host: "--filterRNAstrand forward --effectiveGenomeSize 2913022398 " 
     threads: 4
 
 

workflow/rules/minimap2.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 minimap2:
+    input:
+        fastq = minimap2_input,
+        fasta = minimap2_genome
+    output:
+        sort = minimap2_sort,
+        bam = temp(minimap2_bam)
+    singularity:
+        "rnaflow.img"
+    log:
+        err = minimap2_logs_err,
+        out = minimap2_logs_out
+    params:
+        options = minimap2_options
+    threads:
+        config["minimap2"]["threads"]
+    envmodules:
+        "minimap2/2.17",
+        "samtools"
+    shell:
+        """
+        minimap2 {params.options} -t {threads} {input.fasta} {input.fastq}  | samtools view -Sbh - > {output.bam} 
+        samtools sort -o {output.sort} {output.bam}
+        samtools index {output.sort}
+
+        
+        """