From 33a80bfa42ad558c3a1fd6a8b6aba6de391dc8bb Mon Sep 17 00:00:00 2001
From: seehagec01 <seehagec01@fu-berlin.de>
Date: Mon, 21 Mar 2022 12:06:44 +0100
Subject: [PATCH] fix#1
---
tutorial/config/config.yaml | 4 +++-
tutorial/resources/adapter/TruSeq3-PE.fa | 4 ++++
tutorial/resources/sample/samples.tsv | 7 +++++++
tutorial/workflow/Snakefile | 6 ++++++
tutorial/workflow/envs/yourenv.yaml | 5 +++--
tutorial/workflow/rules/bowtie.smk | 4 ++--
tutorial/workflow/rules/samtools.smk | 3 +--
tutorial/workflow/rules/trimming.smk | 13 +++++++++++--
8 files changed, 37 insertions(+), 9 deletions(-)
create mode 100644 tutorial/resources/adapter/TruSeq3-PE.fa
create mode 100644 tutorial/resources/sample/samples.tsv
diff --git a/tutorial/config/config.yaml b/tutorial/config/config.yaml
index 8442899..37cdf79 100644
--- a/tutorial/config/config.yaml
+++ b/tutorial/config/config.yaml
@@ -1,7 +1,7 @@
---
index: "results/reference/index"
-samples: "resources/samples.tsv"
+samples: "resources/sample/samples.tsv"
bowtieparams: "-q"
@@ -10,3 +10,5 @@ bowtie:
N: 0 # Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
L: 22 # Sets the length of the seed substrings to align during multiseed alignment.
extra: "--ignore-quals --end-to-end" # users can put here all other parameters or simply leave empty
+
+adapter: "resources/adapter/TruSeq3-PE.fa"
diff --git a/tutorial/resources/adapter/TruSeq3-PE.fa b/tutorial/resources/adapter/TruSeq3-PE.fa
new file mode 100644
index 0000000..f38a9d5
--- /dev/null
+++ b/tutorial/resources/adapter/TruSeq3-PE.fa
@@ -0,0 +1,4 @@
+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
diff --git a/tutorial/resources/sample/samples.tsv b/tutorial/resources/sample/samples.tsv
new file mode 100644
index 0000000..fbcea5f
--- /dev/null
+++ b/tutorial/resources/sample/samples.tsv
@@ -0,0 +1,7 @@
+sample fq1 fq2
+ERR024604 results/fastq/ERR024604_1.fastq.gz results/fastq/ERR024604_2.fastq.gz
+ERR024605 results/fastq/ERR024605_1.fastq.gz results/fastq/ERR024605_2.fastq.gz
+ERR024606 results/fastq/ERR024606_1.fastq.gz results/fastq/ERR024606_2.fastq.gz
+ERR024607 results/fastq/ERR024607_1.fastq.gz results/fastq/ERR024607_2.fastq.gz
+ERR024608 results/fastq/ERR024608_1.fastq.gz results/fastq/ERR024608_2.fastq.gz
+ERR024609 results/fastq/ERR024609_1.fastq.gz results/fastq/ERR024609_2.fastq.gz
diff --git a/tutorial/workflow/Snakefile b/tutorial/workflow/Snakefile
index 70a6239..d20a56c 100644
--- a/tutorial/workflow/Snakefile
+++ b/tutorial/workflow/Snakefile
@@ -6,6 +6,10 @@ samples = pd.read_table(config["samples"], index_col="sample")
rule all:
input:
+ expand("results/trimmed/{sample}_forward_paired.fq.gz", sample=samples.index),
+ expand("results/trimmed/{sample}_forward_unpaired.fq.gz", sample=samples.index),
+ expand("results/trimmed/{sample}_reverse_paired.fq.gz", sample=samples.index),
+ expand("results/trimmed/{sample}_reverse_unpaired.fq.gz", sample=samples.index),
"results/aggregate/mappedcounts.csv",
expand("results/stats/{sample}.stats.txt", sample=samples.index),
expand("results/fastqc/{sample}_1_fastqc.html", sample=samples.index),
@@ -20,3 +24,5 @@ include:"rules/bowtie.smk"
include:"rules/samtools.smk"
include:"rules/aggregate.smk"
+
+include:"rules/trimming.smk"
diff --git a/tutorial/workflow/envs/yourenv.yaml b/tutorial/workflow/envs/yourenv.yaml
index fb2f959..bba82dd 100644
--- a/tutorial/workflow/envs/yourenv.yaml
+++ b/tutorial/workflow/envs/yourenv.yaml
@@ -3,6 +3,7 @@ channels:
- bioconda
- defaults
dependencies:
+ - pandas=1.3.5
- bowtie2=2.3.5.1=py37h2dec4b4_0
- c-ares=1.18.1=hca72f7f_0
- ca-certificates=2022.2.1=hecd8cb5_0
@@ -22,10 +23,10 @@ dependencies:
- pip=21.2.2=py37hecd8cb5_0
- python=3.7.11=h88f2d9e_0
- readline=8.1.2=hca72f7f_1
- - samtools=1.4.1=0
+ - samtools=1.3.1=0
- setuptools=58.0.4=py37hecd8cb5_0
- sqlite=3.37.2=h707629a_0
- - tbb=2021.5.0=haf03e11_0
+ - tbb=2020.2
- tk=8.6.11=h7bc2e8c_0
- wheel=0.37.1=pyhd3eb1b0_0
- xz=5.2.5=h1de35cc_0
diff --git a/tutorial/workflow/rules/bowtie.smk b/tutorial/workflow/rules/bowtie.smk
index b60c52e..de9b355 100644
--- a/tutorial/workflow/rules/bowtie.smk
+++ b/tutorial/workflow/rules/bowtie.smk
@@ -16,8 +16,8 @@ rule refindex:
rule map:
input:
"results/reference/index.bt2",
- r1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' ',
- r2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' '
+ "results/trimmed/{sample}_forward_paired.fq.gz",
+ "results/trimmed/{sample}_reverse_paired.fq.gz"
params:
prefix=config["index"],
bowtieparams=config["bowtieparams"]
diff --git a/tutorial/workflow/rules/samtools.smk b/tutorial/workflow/rules/samtools.smk
index dc63db9..5c1d010 100644
--- a/tutorial/workflow/rules/samtools.smk
+++ b/tutorial/workflow/rules/samtools.smk
@@ -42,8 +42,7 @@ rule stats:
"results/bam_sorted/{sample}.bam.bai"
output:
"results/stats/{sample}.stats.txt"
- threads:4
conda:
"../envs/yourenv.yaml"
shell:
- "samtools idxstats --threads={threads} {input[0]} > {output}"
+ "samtools idxstats {input[0]} > {output}"
diff --git a/tutorial/workflow/rules/trimming.smk b/tutorial/workflow/rules/trimming.smk
index 9ee44de..f2fb3f1 100644
--- a/tutorial/workflow/rules/trimming.smk
+++ b/tutorial/workflow/rules/trimming.smk
@@ -2,7 +2,16 @@ rule trimming:
input:
rt1 = lambda wildcards: samples.at[wildcards.sample,'fq1'] if wildcards.sample in samples.index else ' ',
rt2 = lambda wildcards: samples.at[wildcards.sample,'fq2'] if wildcards.sample in samples.index else ' '
+ params:
+ adapter=config["adapter"]
output:
- "results/trimmed/{sample}.fq.gz"
+ "results/trimmed/{sample}_forward_paired.fq.gz",
+ "results/trimmed/{sample}_forward_unpaired.fq.gz",
+ "results/trimmed/{sample}_reverse_paired.fq.gz",
+ "results/trimmed/{sample}_reverse_unpaired.fq.gz"
+ conda:
+ "../envs/yourenv.yaml"
+ log:
+ "workflow/report/trimming/{sample}.log"
shell:
- "java -jar trimmomatic-0.39.jar PE {input[0]} {input[1]} {output} ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36"
+ "trimmomatic PE {input[0]} {input[1]} {output} ILLUMINACLIP:{params.adapter}:2:30:10:2:True LEADING:3 TRAILING:3 MINLEN:36"
--
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