From 8ee4c5adbc8bc1036e412c28cc358dfbf5169bb8 Mon Sep 17 00:00:00 2001
From: rlegendr <rachel.legendre@pasteur.fr>
Date: Fri, 17 Sep 2021 16:58:08 +0200
Subject: [PATCH] add minimap2
---
config/config.yaml | 28 +++++++++++++++++--
workflow/rules/minimap2.rules | 52 +++++++++++++++++++++++++++++++++++
2 files changed, 77 insertions(+), 3 deletions(-)
create mode 100755 workflow/rules/minimap2.rules
diff --git a/config/config.yaml b/config/config.yaml
index 02693fd..d3e76ee 100644
--- a/config/config.yaml
+++ b/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
diff --git a/workflow/rules/minimap2.rules b/workflow/rules/minimap2.rules
new file mode 100755
index 0000000..d4f7325
--- /dev/null
+++ b/workflow/rules/minimap2.rules
@@ -0,0 +1,52 @@
+#########################################################################
+# 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}
+
+
+ """
--
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