From 1b4bdf84e04c9679f70deb8a0d4c1e545e9d9334 Mon Sep 17 00:00:00 2001
From: rlegendre <rachel.legendre@pasteur.fr>
Date: Fri, 30 Dec 2022 14:30:38 +0100
Subject: [PATCH] rename adapters options
---
README.md | 26 ++++++++++++++------------
Snakefile | 3 ++-
config/config.yaml | 4 ++--
3 files changed, 18 insertions(+), 15 deletions(-)
diff --git a/README.md b/README.md
index d34a20a..5ea7a14 100644
--- a/README.md
+++ b/README.md
@@ -136,7 +136,7 @@ run it in NNCR using environment modules via
- Genome information
-fill only the first lines relative to the first genome
+Fill only the four first lines relative to the first genome with your eukaryotic genome. No need to fill "host_" information when host_mapping is set to no : lines will be ignored by the pipeline. In any case, no need to comment a line in the config.yaml, it will broke the pipeline.
```
genome:
@@ -163,8 +163,8 @@ adapters:
alien_file: config/TruSeq_Stranded_RNA.fa
m: 25
mode: b
- #options: -O 6 --trim-n --max-n 1 # for cutadapt
- options: -k 10 -m 5 -p 80 # for alienTrimmer
+ options_cutadapt: -O 6 --trim-n --max-n 1
+ options_alien: -k 10 -m 5 -p 80
quality: 30
threads: 4
@@ -196,9 +196,10 @@ Other tools are set to 'no'
Why counting with Salmon and not STAR ? some informations here :
-https://www.sciencedirect.com/science/article/pii/S2001037020303032
-https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001
-https://f1000research.com/articles/4-1521/v2
+
+- https://www.sciencedirect.com/science/article/pii/S2001037020303032
+- https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0141910#pone-0141910-t001
+- https://f1000research.com/articles/4-1521/v2
@@ -206,7 +207,7 @@ https://f1000research.com/articles/4-1521/v2
- Genome information
-fill the genome section with pathogen and host genomes
+Fill the genome section with pathogen and host genomes (fasta and gff)
```
genome:
@@ -233,8 +234,8 @@ adapters:
alien_file: config/TruSeq_Stranded_RNA.fa
m: 25
mode: b
- #options: -O 6 --trim-n --max-n 1 # for cutadapt
- options: -k 10 -m 5 -p 80 # for alienTrimmer
+ options_cutadapt: -O 6 --trim-n --max-n 1
+ options_alien: -k 10 -m 5 -p 80
quality: 30
threads: 4
@@ -282,7 +283,8 @@ Other tools are set to 'no'
- Genome information
-fill the genome section with bacteria information
+Fill only the four first lines relative to the first genome with your prokaryotic genome. No need to fill "host_" information when host_mapping is set to no : lines will be ignored by the pipeline. In any case, no need to comment a line in the config.yaml, it will broke the pipeline.
+
```
genome:
@@ -309,8 +311,8 @@ adapters:
alien_file: config/TruSeq_Stranded_RNA.fa
m: 25
mode: b
- #options: -O 6 --trim-n --max-n 1 # for cutadapt
- options: -k 10 -m 5 -p 80 # for alienTrimmer
+ options_cutadapt: -O 6 --trim-n --max-n 1
+ options_alien: -k 10 -m 5 -p 80
quality: 30
threads: 4
diff --git a/Snakefile b/Snakefile
index 2f9142b..498f0f1 100755
--- a/Snakefile
+++ b/Snakefile
@@ -109,15 +109,16 @@ if config["adapters"]["remove"] :
adapters_output += [os.path.join(analysis_dir, "01-Trimming/{{SAMPLE}}{}_trim.fastq".format(rt2))]
# Set parameters
- adapters_options = config["adapters"]["options"]
adapters_mode = config["adapters"]["mode"]
adapters_min = config["adapters"]["m"]
adapters_qual = config["adapters"]["quality"]
adapters_log = os.path.join(analysis_dir, "01-Trimming/logs/{SAMPLE}_trim.txt")
#final_output.extend(expand(adapters_output, SAMPLE=samples))
if adapter_tool == "cutadapt" :
+ adapters_options = config["adapters"]["options_cutadapt"]
include: os.path.join(RULES, "cutadapt.rules")
elif adapter_tool == "alienTrimmer" :
+ adapters_options = config["adapters"]["options_alien"]
include: os.path.join(RULES, "alienTrimmer.rules")
else :
raise ValueError("Please provides an implemented removal adapter tool: must be cutadapt or alienTrimer")
diff --git a/config/config.yaml b/config/config.yaml
index 56ed5b3..4850190 100755
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -128,8 +128,8 @@ adapters:
alien_file: config/TruSeq_Stranded_RNA.fa
m: 25
mode: b
- #options: -O 6 --trim-n --max-n 1 # for cutadapt
- options: -k 10 -m 5 -p 80 # for alienTrimmer
+ options_cutadapt: -O 6 --trim-n --max-n 1
+ options_alien: -k 10 -m 5 -p 80
quality: 30
threads: 4
--
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