fix#1

tutorial/config/config.yaml

 ---
 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"

tutorial/resources/adapter/TruSeq3-PE.fa

+>PrefixPE/1
+TACACTCTTTCCCTACACGACGCTCTTCCGATCT
+>PrefixPE/2
+GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT

tutorial/resources/sample/samples.tsv

+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

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"

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

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"]

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}"

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"