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ruilulab · Jan 21, 2020 · dcbfee2 · dcbfee2
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commit dcbfee2
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Showing 10 changed files with 59 additions and 2 deletions.
diff --git a/bowtie2-macs2-homer.snakefile → bowtie2-macs2-homer.smk b/bowtie2-macs2-homer.snakefile → bowtie2-macs2-homer.smk
diff --git a/config.yml b/config.yml
@@ -32,7 +32,7 @@ workdir: "/home/fangzq/projects/bulk"
 scripts: "/home/fangzq/github/snakeflow/scripts"
 
 # Full path to a folder that holds all of your FASTQ files
-fastq_dir: "/home/mwang024/ARPKD/Data/bulk"
+fastq_dir: "/data/bases/shared/bulk_RNA_seq/30_225476525_trim"
 
 
 

diff --git a/hisat2-rmats-turbo-v0.1.snakefile → hisat2-rmats-turbo-v0.1.smk b/hisat2-rmats-turbo-v0.1.snakefile → hisat2-rmats-turbo-v0.1.smk
diff --git a/hisat2-rseqc-fastqc-multiqc.snakefile → hisat2-rseqc-fastqc-multiqc.smk b/hisat2-rseqc-fastqc-multiqc.snakefile → hisat2-rseqc-fastqc-multiqc.smk
diff --git a/hisat2-stringtie-ballgown-v0.1.snakefile → hisat2-stringtie-ballgown-v0.1.smk b/hisat2-stringtie-ballgown-v0.1.snakefile → hisat2-stringtie-ballgown-v0.1.smk
diff --git a/rmats2sashimi.snakefile → rmats2sashimi.smk b/rmats2sashimi.snakefile → rmats2sashimi.smk
diff --git a/rules/fastp.rules b/rules/fastp.rules
@@ -0,0 +1,45 @@
+rule trim_galore:
+    input: 
+        r1=join(FASTQ_RAW,"{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_RAW,"{sample}_R2.fastq.gz"),
+    output:
+        r1=join(FASTQ_CLEAN, "{sample}_R1_val_1.fastq.gz"),
+        r2=join(FASTQ_CLEAN, "{sample}_R2_val_2.fastq.gz"),
+
+    log: "logs/trim-galore/${sample}.trimgalore.log"
+    params:
+        outdir="fastq_clean",
+        fastqc_outdir="qc/fastqc_clean"
+    shell:
+        "trim_galore -q 20 --phred33  --stringency 1 -e 0.1  --length 50 --paired " 
+        "-o {params.outdir}  {input.r1} {input.r2} > {log}"
+
+rule trimmonatic:
+    input:
+        r1=join(FASTQ_RAW, "{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_RAW, "{sample}_R2.fastq.gz"),
+        adap=config['adaptors']['illumina']
+    output:
+        r1=join(FASTQ_CLEAN, "{sample}_R1_val_1.fastq.gz"),
+        r2=join(FASTQ_CLEAN, "{sample}_R2_val_2.fastq.gz"),
+        r1up=join(FASTQ_CLEAN, "{sample}_R1_val_upparied_1.fastq.gz"),
+        r2up=join(FASTQ_CLEAN, "{sample}_R1_val_upparied_2.fastq.gz)"
+    log: "logs/trimmonatic/${sample}.trimmonatic.log"
+    thread: 8
+    shell:
+        "trimmomatic PE -threads {thread} -phred33 {output.r1} {ouput.upr1} {output.r2} {ouput.upr2} "
+        "LLUMINACLIP:{input.adap}:2:30:10 LEADING:10 TRAILING:20 SLIDINGWINDOW:4:25 MINLEN:50 "
+        "| tee {log} "
+
+rule fastp:
+    input:
+        r1=join(FASTQ_RAW, "{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_RAW, "{sample}_R2.fastq.gz"),   
+    output:
+        r1=join(FASTQ_CLEAN, "{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_CLEAN, "{sample}_R2.fastq.gz"),
+    tread: 8
+    params:
+    log: "logs/fastp/${sample}.fastp.log"
+    shell:
+        "fastp -q 20 --thread {thread} -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} --html {wildcards.sample}.html 2> {log}" 
diff --git a/rules/trim_reads.rules b/rules/trim_reads.rules
@@ -32,4 +32,16 @@ rule trimmonatic:
     shell:
         "trimmomatic PE -threads {thread} -phred33 {output.r1} {ouput.upr1} {output.r2} {ouput.upr2} "
         "LLUMINACLIP:{input.adap}:2:30:10 LEADING:10 TRAILING:20 SLIDINGWINDOW:4:25 MINLEN:50 "
-        "| tee {log} "
+        "| tee {log} "
+
+rule fastp:
+    input:
+        r1=join(FASTQ_RAW, "{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_RAW, "{sample}_R2.fastq.gz"),   
+    output:
+        r1=join(FASTQ_CLEAN,"{sample}_R1.fastq.gz"),
+        r2=join(FASTQ_CLEAN,"{sample}_R2.fastq.gz"),
+    tread: 8
+    log: "logs/fastp/${sample}.fastp.log"
+    shell:
+        "fastp -q 20 --thread {thread} -i {input.r1} -I {input.r2} -o {output.r1} -O {output.r2} 2> {log}" 
diff --git a/salmon-tximport-deseq2-docker.snakeflie → salmon-tximport-deseq2-docker.smk b/salmon-tximport-deseq2-docker.snakeflie → salmon-tximport-deseq2-docker.smk
diff --git a/salmon-tximport-deseq2-v0.3.snakefile → salmon-tximport-deseq2-v0.3.smk b/salmon-tximport-deseq2-v0.3.snakefile → salmon-tximport-deseq2-v0.3.smk