Entering edit mode
4.9 years ago
arshil
•
0
Hi everyone, can someone help me out with the error. i am running the following code for my fastq files, when i run , only the fastqc rule is excuted and its says job completed, my two other rules for trimming and fastqc for trimmed files doesnt get executed. i am pretty new to bioinformatics. my codes looks like.
SAMPLES, = glob_wildcards("/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz")
READS=["1", "2"]
rule fastqc_raw:
input: "/scratch/mk9uc/RNA_Seq/{sample}_{read}.fastq.gz"
output: "qc_outputt/{sample}_{read}_fastqc.html"
shell: """
module load fastqc
mkdir -p qc_outputt
fastqc --outdir qc_outputt --thread 8 --nogroup {input}
# >> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>{log}
"""
rule trimming:
input:
fwd = "/scratch/mk9uc/RNA_Seq/{sample}_1.fastq.gz",
rev = "/scratch/mk9uc/RNA_Seq/{sample}_2.fastq.gz"
output:
fwd_paired = "seqs_trimmedd/{sample}_trimmed_1.fastq.gz",
rev_paired = "seqs_trimmedd/{sample}_trimmed_2.fastq.gz",
params:
PAIR = "PE SE".split(),
TRIM_OPTS = " -threads 16 -phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"
shell: """
module load trimmomatic
mkdir -p seqs_trimmedd
java -jar $EBROOTTRIMMOMATIC/trimmomatic-0.36.jar \
{params.PAIR[0]} {input.fwd} {input.rev} \
{output.fwd_paired} \
{output.rev_paired} \
{params.TRIM_OPTS}
"""
rule fastqc_trimmed:
input: "/scratch/mk9uc/RNA_Seq/seqs_trimmedd/{sample}_trimmed_{read}.fastq.gz"
output: "trimmedd/qc_output/{sample}_{read}_fastqc.html"
shell: """
module load fastqc
mkdir -p qc_trimmedd
fastqc --outdir qc_trimmedd --thread 8 --nogroup {input}
# >> /scratch/mk9uc/RNA_Seq/fastqc.log 2>>{log}
"""
rule mytarget:
input: expand("qc_outputt/{sample}_{read}_fastqc.html", sample=SAMPLES, read=READS)
input: expand("seqs_trimmedd/{sample}_trimmed_{read}.fastq.gz", sample=SAMPLES, read=READS)
input: expand("qc_trimmedd/{sample}_{read}_fastqc.html", sample=SAMPLES, read=READS)