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ATAC-seq_pipeline/labjournal/19-11-2020.md

+```
+rule trimmomatic:
+    input:
+        reads = get_fastq,
+        adapters = config['trimmomatic']["adapters"]
+    output:
+        forward_reads   = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
+        reverse_reads   = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz",
+        forwardUnpaired = temp(WORKING_DIR + "trimmed/{samples}_forward_unpaired.fastq.gz"),
+        reverseUnpaired = temp(WORKING_DIR + "trimmed/{samples}_reverse_unpaired.fastq.gz"),
+    log:
+        RESULT_DIR + "logs/trimmomatic/{samples}.log"
+    params:
+        seedMisMatches =            str(config['trimmomatic']['seedMisMatches']),
+        palindromeClipTreshold =    str(config['trimmomatic']['palindromeClipTreshold']),
+        simpleClipThreshhold =      str(config['trimmomatic']['simpleClipThreshold']),
+        LeadMinTrimQual =           str(config['trimmomatic']['LeadMinTrimQual']),
+        TrailMinTrimQual =          str(config['trimmomatic']['TrailMinTrimQual']),
+        windowSize =                str(config['trimmomatic']['windowSize']),
+        avgMinQual =                str(config['trimmomatic']['avgMinQual']),
+        minReadLen =                str(config['trimmomatic']['minReadLength']),
+        phred = 		            str(config["trimmomatic"]["phred"])
+    threads: 10
+    conda:
+        "envs/trimmomatic.yaml"
+    shell:
+        """
+        trimmomatic PE \
+        -threads 10 \
+        -phred33 \
+         {input.reads} \
+         {output.forward_reads} {output.forwardUnpaired} {output.reverse_reads} {output.reverseUnpaired} \
+         ILLUMINACLIP:{input.adapters}:{params.seedMisMatches}:{params.palindromeClipTreshold}:{params.simpleClipThreshhold} \
+         LEADING:3 \
+         TRAILING:3 \
+         SLIDINGWINDOW:4:15 \
+         MINLEN:40 &>{log}
+        """
+      ```
+  ####Trimmomatic Arguments####

ATAC-seq_pipeline/snakefile

@@ -46,9 +46,11 @@ wildcard_constraints:
 FASTQC          = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.html", samples = SAMPLES, R=['R1', 'R2']),
 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']),
+TRIMMED_FASTQC  = expand(RESULT_DIR + "trimmed_fastqc/WT8_{direction}_fastqc.html", direction=['forward', 'reverse']),
 MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
 UNMAPPED = expand([WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)], samples = SAMPLES),
+MAP_SORTED = expand(WORKING_DIR + "sort/{samples}.sorted.bam", samples = SAMPLES),
+SORTED_INDEXED = expand(WORKING_DIR + "index/{samples}.sorted.bam.bai", samples = SAMPLES)
 
 rule all:
     input:
@@ -61,7 +63,9 @@ rule all:
         REVERSE_READS,
         TRIMMED_FASTQC,
         MAPPED,
-        UNMAPPED
+        UNMAPPED,
+        MAP_SORTED,
+        SORTED_INDEXED
     message : "Analysis is complete!"
     shell:""
 
@@ -127,18 +131,18 @@ rule trimmomatic:
 
 rule trimmed_fastqc:
     input:
-        forward_reads   = WORKING_DIR + "trimmed/{samples}_forward.fastq.gz",
-        reverse_reads   = WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz"
+        WT8forward = WORKING_DIR + "trimmed/WT8_forward.fastq.gz",
+        WT8reverse = WORKING_DIR + "trimmed/WT8_reverse.fastq.gz"
     output:
-        RESULT_DIR + "fastqc/{samples}_{R}_trimmed_fastqc.html"
-    log:
-        RESULT_DIR + "logs/fastqc/{samples}.trimmed_fastqc.log"
+        RESULT_DIR + "trimmed_fastqc/WT8_{direction}_fastqc.html"
     params:
-        RESULT_DIR + "fastqc/"
+        RESULT_DIR + "trimmed_fastqc/"
     conda:
         "envs/fastqc.yaml"
+    log:
+        RESULT_DIR + "logs/trimmed_fastqc/WT8_{direction}.fastqc.log"
     shell:
-        "fastqc --outdir={params} {input.forward_reads} {input.reverse_reads} &>{log}"
+        "fastqc --outdir={params} {input.WT8forward} {input.WT8reverse} &>{log}"
 
 rule fastqc:
     input:
@@ -178,3 +182,27 @@ rule mapping:
         """
         bowtie2 {params.bowtie} --threads {threads} -x {params.index} -1 {input.forward_reads} -2 {input.reverse_reads} -U {input.forwardUnpaired},{input.reverseUnpaired} --un-conc-gz {params.unmapped} | samtools view -Sb - > {output.mapped} 2>{log}
         """
+
+rule sort:
+    input:
+        mapped = WORKING_DIR + "mapped/{samples}.bam"
+    output:
+        map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
+    conda:
+        "envs/samtools_bowtie.yaml"
+    log:
+        RESULT_DIR + "logs/sort/{samples}.log"
+    shell:
+        "samtools sort {input} -o {output}"
+
+rule index:
+    input:
+        map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
+    output:
+        sorted_indexed = WORKING_DIR + "index/{samples}.sorted.bam.bai"
+    conda:
+        "envs/samtools_bowtie.yaml"
+    log:
+        RESULT_DIR + "logs/index/{samples}.log"
+    shell:
+        "samtools index {input} {output}"