solved an error in rule trimmomatic

ATAC-seq_pipeline/config.yaml

@@ -26,3 +26,12 @@ trimmomatic:
   avgMinQual:             '15'
   minReadLength:          '40'
   phred:                  '-phred33'
+
+# bowtie2 parameters
+bowtie2:
+  params:
+    mode:             "--local"
+    sensitivity:      "--very-sensitive-local"
+    max_fragment_len: "--maxins 500"                # maximum fragment length for valid paired-end alignments
+    min_fragment_len: "--minins 80"                 # minimum fragment length for valid paired-end alignments
+    verbose:          "-q"

ATAC-seq_pipeline/envs/samtools_bowtie.yaml

@@ -2,3 +2,4 @@ channels:
   - bioconda
 dependencies:
   - bowtie2=2.3.5
+  - samtools=1.9

ATAC-seq_pipeline/snakefile

@@ -47,7 +47,8 @@ FASTQC          = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.htm
 FORWARD_READS   = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
 REVERSE_READS   = expand(WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz", samples = SAMPLES),
 TRIMMED_FASTQC  = expand(RESULT_DIR + "fastqc/{samples}_{R}_trimmed_fastqc.html", samples = SAMPLES, R=['R1', 'R2']),
-
+MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
+UNMAPPED = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
 
 rule all:
     input:
@@ -58,7 +59,9 @@ rule all:
         WORKING_DIR + "genome.rev.2.bt2",
         FORWARD_READS,
         REVERSE_READS,
-        TRIMMED_FASTQC,
+        #TRIMMED_FASTQC,
+        #MAPPED,
+        #UNMAPPED
     message : "Analysis is complete!"
     shell:""
 
@@ -110,7 +113,7 @@ rule trimmomatic:
         "envs/trimmomatic.yaml"
     shell:
         """
-        java -jar trimmomatic-0.32.jar PE \
+        trimmomatic PE \
         -threads 10 \
         -phred33 \
          {input.reads} \
@@ -148,3 +151,27 @@ rule fastqc:
         "envs/fastqc.yaml"
     shell:
         "fastqc --outdir={params} {input.fwd} {input.rev} &>{log}"
+
+rule mapping:
+    input:
+        foward = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
+        reverse = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
+        forwardUnpaired = WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz",
+        reverseUnpaired = WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz",
+        index = [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)]
+    output:
+        mapped = WORKING_DIR + "mapped/{samples}.bam",
+        unmapped = [WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)],
+    params:
+        bowtie          = " ".join(config["bowtie2"]["params"].values()), #take argument separated as a list separated with a space
+        index           = WORKING_DIR + "genome",
+        unmapped        = WORKING_DIR + "unmapped/{samples}.fq.gz"
+    threads: 10
+    conda:
+        "../envs/samtools_bowtie.yaml"
+    log:
+        RESULT_DIR + "logs/bowtie/{samples}.log"
+    shell:
+        """
+        bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward} -2 {input.reverse} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>{log}
+        """