working pipeline for fastqc and index_genome

.gitignore

+.DS_Store
+ATAC-seq_pipeline/temp/*

ATAC-seq_pipeline/config.yaml

+## directories ##
+
+working_dir: "temp/"
+
+results_dir: "results/"
+
+data_dir: "../data/"
+
+sample : "units.tsv"
+
+## genome reference ##
+
+genome_fasta_url : "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M17/GRCm38.primary_assembly.genome.fa.gz"
+
+
+
+## trimmomatic ##
+
+adapters: "adapters.fasta"

ATAC-seq_pipeline/envs/fastqc.yaml

+channels:
+  - bioconda
+dependencies:
+  - fastqc=0.11.9

ATAC-seq_pipeline/envs/samtools_bowtie.yaml

+channels:
+  - bioconda
+dependencies:
+  - bowtie2=2.4.2
+  - samtools=1.11

ATAC-seq_pipeline/rules

+#######Configuration files#######
+
+
+
+GENOME_FASTA_URL = config[‘genome_fasta_url’]
+
+WORKING_DIR = config[working_dir]
+
+RESULT_DIR = config[results_dir]
+
+
+
+
+
+#######Rules###########
+
+
+
+rule download_genome:
+
+output:
+
+WORKING_DIR + “reference.fa”
+
+shell:
+
+“wget -o {output} {GENOME_FASTA_URL}”
+
+
+
+# download the file from GENOME_FASTA_URL link and save the file to {output}
+
+
+
+rule fastqc:
+
+input:
+
+fwd = WORKING_DIR + “{samples}_fwd.fq”
+
+rev = WORKING_DIR + “{samples}_rev.fq”
+
+output:
+
+R1 = RESULT_DIR + “fastqc/{samples}_fwd.fq.gz”
+
+R2 = RESULT_DIR + “fastqc/{samples}_rev.fq.gz”
+
+shell:
+
+“fastqc -o {output} -t 10 {input}”
+
+
+
+# fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam] [-c contaminant file] seqfile1 .. seqfileN
+
+
+
+rule trimmomatic:
+
+input:
+
+R1 = RESULT_DIR + “fastqc/{samples}_fwd.fq.gz”
+
+R2 = RESULT_DIR + “fastqc/{samples}_rev.fq.gz”
+
+output:
+
+forward = WORKING_DIR + “trimmed/{samples}_forward.fq.gz”
+
+reverse = WORKING_DIR + “trimmed/{samples}_reverse.fq.gz”
+
+shell:
+
+“java -jar trimmomatic-0.35.jar PE -phred33 {input} {output}”
+
+
+
+rule fastqc2:
+
+input:
+
+forward = WORKING_DIR + “trimmed/{samples}_forward.fq.gz”
+
+reverse = WORKING_DIR + “trimmed/{samples}_reverse.fq.gz”output:
+
+RESULT_DIR + “fastqc/{samples}_forward_posttrim.fq.gz”
+
+RESULT_DIR + “fastqc/{samples}_reverse_posttrim.fq.gz”
+
+shell:
+
+“fastqc -o {output} -t 6 {input}”
+
+
+
+rule index:
+
+input:
+
+WORKING_DIR + “reference.fa”
+
+output:
+
+WORKING_DIR + “genome.rev.1.bt2”
+
+WORKING_DIR + “genome.rev.2.bt2”
+
+message:
+
+“index reference genome”
+
+params:
+
+WORKING_DIR + “genome_index”
+
+shell:
+
+“bowtie2-build –threads 10 {input}{params}”
+
+
+
+rule align:
+
+input:
+
+index = WORKING_DIR + “genome_index”
+
+forward = WORKING_DIR + “trimmed/{samples}_forward.fq.gz”
+
+reverse = WORKING_DIR + “trimmed/{samples}_reverse.fq.gz”
+
+params:
+
+index = WORKING_DIR + “genome_index”
+
+output:
+
+WORKING_DIR + “mapped/{sample}.bam”
+
+message:
+
+“mapping samples to reference genome”
+
+shell:
+
+“bowtie2 -t 10 {params.index} -1 {input.forward} -2{input.reverse} | samtools view -Sb - > {output}”

ATAC-seq_pipeline/snakefile

+################## Import libraries ##################
+
+import pandas as pd
+import os
+import sys
+from subprocess import call
+import itertools
+from snakemake.utils import R
+
+
+################## Configuration file and PATHS##################
+
+configfile: "config.yaml"
+
+WORKING_DIR         = config["working_dir"]
+RESULT_DIR          = config["results_dir"]
+DATA_DIR            = config["data_dir"]
+GENOME_FASTA_URL    = config["genome_fasta_url"]
+
+#units = pd.read_table(config["units"], dtype=str).set_index(["bed"], drop=False)
+
+#BED = units.index.get_level_values('bed').unique().tolist()
+
+units = pd.read_table(config["sample"], dtype=str).set_index(["sample"], drop=False)
+
+SAMPLES = units.index.get_level_values('sample').unique().tolist()
+
+###############
+# Helper Functions
+###############
+def get_fastq(wildcards):
+    return units.loc[(sample), ["fq1", "fq2"]].dropna()
+
+################## DESIRED OUTPUT ##################
+
+FASTQC  = expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.html", samples = SAMPLES, R=['R1', 'R2'])
+
+
+
+rule all:
+    input:
+        FASTQC,
+        WORKING_DIR + "reference",
+        [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)],
+        WORKING_DIR + "genome.rev.1.bt2",
+        WORKING_DIR + "genome.rev.2.bt2"
+    message : "Analysis is complete!"
+    shell:""
+
+################## INCLUDE RULES ##################
+rule download_genome:
+    output:
+        WORKING_DIR + "reference",
+    shell:
+        "wget -O {output} {GENOME_FASTA_URL}"
+
+rule index_genome:
+    input:
+        WORKING_DIR + "reference",
+    output:
+        [WORKING_DIR + "genome." + str(i) + ".bt2" for i in range(1,4)],
+        WORKING_DIR + "genome.rev.1.bt2",
+        WORKING_DIR + "genome.rev.2.bt2"
+    message:"Indexing Reference genome"
+    params:
+        WORKING_DIR + "genome"
+    conda:
+        "envs/samtools_bowtie.yaml"
+    shell:
+        "bowtie2-build --threads 10 {input} {params}"
+
+rule trimmomatic:
+    input:
+        
+
+rule fastqc:
+    input:
+        fwd = expand(DATA_DIR + "{samples}_R1_2000reads.fq.gz", samples = SAMPLES),
+        rev = expand(DATA_DIR + "{samples}_R2_2000reads.fq.gz", samples = SAMPLES)
+    output:
+        expand(RESULT_DIR + "fastqc/{samples}_{R}_2000reads_fastqc.html", samples = SAMPLES, R=['R1', 'R2'])
+    log:
+        expand(RESULT_DIR + "logs/fastqc/{samples}.fastqc.log", samples = SAMPLES)
+    params:
+        RESULT_DIR + "fastqc/"
+    conda:
+        "envs/fastqc.yaml"
+    shell:
+        "fastqc --outdir={params} {input.fwd} {input.rev} &>{log}"

ATAC-seq_pipeline/units.tsv

+sample	fq1	fq2
+WT8	../data/WT8_R1_2000reads.fq.gz	../data/WT8_R2_2000reads.fq.gz
+KO12	../data/KO12_R1_10reads.fq.gz	../data/KO12_R2_10reads.fq.gz