Generate all temp files in output directory

liulab-dfci · Jul 16, 2020 · 9373410 · 9373410
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diff --git a/MAESTRO.egg-info/PKG-INFO b/MAESTRO.egg-info/PKG-INFO
@@ -0,0 +1,17 @@
+Metadata-Version: 1.1
+Name: MAESTRO
+Version: 1.2.0
+Summary: MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake.
+Home-page: https://github.com/chenfeiwang/MAESTRO
+Author: Chenfei Wang, Dongqing Sun
+Author-email: UNKNOWN
+License: GPL-3.0
+Description: UNKNOWN
+Platform: UNKNOWN
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: GPL License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
diff --git a/MAESTRO.egg-info/SOURCES.txt b/MAESTRO.egg-info/SOURCES.txt
@@ -0,0 +1,27 @@
+README.md
+setup.py
+MAESTRO/MAESTRO
+MAESTRO/MAESTRO_PipeInit.py
+MAESTRO/__init__.py
+MAESTRO/integrate_HTMLReport.py
+MAESTRO/scATAC_10x_BarcodeCorrect.py
+MAESTRO/scATAC_10x_PeakCount.py
+MAESTRO/scATAC_BamAddTag.py
+MAESTRO/scATAC_FragmentCorrect.py
+MAESTRO/scATAC_FragmentGenerate.py
+MAESTRO/scATAC_Genescore.py
+MAESTRO/scATAC_H5Process.py
+MAESTRO/scATAC_HTMLReport.py
+MAESTRO/scATAC_QC.py
+MAESTRO/scATAC_microfluidic_PeakCount.py
+MAESTRO/scATAC_microfluidic_QC.py
+MAESTRO/scATAC_sci_BarcodeExtract.py
+MAESTRO/scATAC_utility.py
+MAESTRO/scRNA_AnalysisPipeline.py
+MAESTRO/scRNA_HTMLReport.py
+MAESTRO/scRNA_QC.py
+MAESTRO/scRNA_utility.py
+MAESTRO.egg-info/PKG-INFO
+MAESTRO.egg-info/SOURCES.txt
+MAESTRO.egg-info/dependency_links.txt
+MAESTRO.egg-info/top_level.txt
diff --git a/MAESTRO.egg-info/dependency_links.txt b/MAESTRO.egg-info/dependency_links.txt
@@ -0,0 +1 @@
+
diff --git a/MAESTRO.egg-info/top_level.txt b/MAESTRO.egg-info/top_level.txt
@@ -0,0 +1 @@
+MAESTRO
diff --git a/MAESTRO/Snakemake/scATAC/Snakefile b/MAESTRO/Snakemake/scATAC/Snakefile
@@ -331,9 +331,9 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
                 fastqs = config["fastqdir"],
                 fasta = config["genome"]["fasta"]
             output:
-                r1cat = temp(os.path.join(config["fastqdir"], "%s_R1.fastq" %(config["fastqprefix"]))),
-                r2cat = temp(os.path.join(config["fastqdir"], "%s_R2.fastq" %(config["fastqprefix"]))),
-                r3cat = temp(os.path.join(config["fastqdir"], "%s_R3.fastq" %(config["fastqprefix"]))),
+                r1cat = temp(os.path.join("Result/Tmp", "%s_R1.fastq" %(config["fastqprefix"]))),
+                r2cat = temp(os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"]))),
+                r3cat = temp(os.path.join("Result/Tmp", "%s_R3.fastq" %(config["fastqprefix"]))),
             params:
                 r1 = getfastq_10x(config["fastqdir"], config["fastqprefix"])["r1"],
                 r2 = getfastq_10x(config["fastqdir"], config["fastqprefix"])["barcode"],
@@ -383,24 +383,41 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
                 fastq1 = os.path.join(config["fastqdir"], "%s_1.fastq" %(config["fastqprefix"])),
                 fastq2 = os.path.join(config["fastqdir"], "%s_2.fastq" %(config["fastqprefix"])),
             output:
+                r1 = temp(os.path.join("Result/Tmp", "%s_R1.fastq" %(config["fastqprefix"]))),
+                r2 = temp(os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"]))),
+                r3 = temp(os.path.join("Result/Tmp", "%s_R3.fastq" %(config["fastqprefix"]))),
+            params:
+                outdir = "Result/Tmp"
+            benchmark:
+                "Result/Benchmark/%s_Preprocess.benchmark" %(config["outprefix"])
+            shell:
+                "python " + SCRIPT_PATH + "/scATAC_sci_BarcodeExtract.py --R1 {input.fastq1} --R2 {input.fastq2} -O {params.outdir}"
+
+        rule scatac_preprocess_fastqrename:
+            input:
+                fasta = config["genome"]["fasta"],
                 r1 = os.path.join(config["fastqdir"], "%s_R1.fastq" %(config["fastqprefix"])),
                 r2 = os.path.join(config["fastqdir"], "%s_R2.fastq" %(config["fastqprefix"])),
                 r3 = os.path.join(config["fastqdir"], "%s_R3.fastq" %(config["fastqprefix"])),
+            output:
+                r1 = temp(os.path.join("Result/Tmp", "%s_R1.fastq" %(config["fastqprefix"]))),
+                r2 = temp(os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"]))),
+                r3 = temp(os.path.join("Result/Tmp", "%s_R3.fastq" %(config["fastqprefix"]))),
             params:
-                outdir = config["fastqdir"]
+                outdir = "Result/Tmp"
             benchmark:
                 "Result/Benchmark/%s_Preprocess.benchmark" %(config["outprefix"])
             shell:
-                "python " + SCRIPT_PATH + "/scATAC_sci_BarcodeExtract.py --R1 {input.fastq1} --R2 {input.fastq2} -O {params.outdir}"
+                "cp {input.r1} {input.r2} {input.r3} {params.outdir};"
 
     rule scatac_fqaddbarcode:
         input:
-            r1 = os.path.join(config["fastqdir"], "%s_R1.fastq" %(config["fastqprefix"])),
-            r2 = os.path.join(config["fastqdir"], "%s_R2.fastq" %(config["fastqprefix"])),
-            r3 = os.path.join(config["fastqdir"], "%s_R3.fastq" %(config["fastqprefix"])),
+            r1 = os.path.join("Result/Tmp", "%s_R1.fastq" %(config["fastqprefix"])),
+            r2 = os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"])),
+            r3 = os.path.join("Result/Tmp", "%s_R3.fastq" %(config["fastqprefix"])),
         output:
-            r1 = temp(os.path.join(config["fastqdir"], "%s_R1.barcoded.fastq" %(config["fastqprefix"]))),
-            r3 = temp(os.path.join(config["fastqdir"], "%s_R3.barcoded.fastq" %(config["fastqprefix"]))),
+            r1 = temp(os.path.join("Result/Tmp", "%s_R1.barcoded.fastq" %(config["fastqprefix"]))),
+            r3 = temp(os.path.join("Result/Tmp", "%s_R3.barcoded.fastq" %(config["fastqprefix"]))),
             # r1 = "%s/%s_R1.barcoded.fastq" %(config["fastqdir"], config["fastqprefix"]),
             # r3 = "%s/%s_R3.barcoded.fastq" %(config["fastqdir"], config["fastqprefix"]),
         benchmark:
@@ -412,8 +429,8 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
     rule scatac_map:
         input:
             fasta = config["genome"]["fasta"],
-            r1 = os.path.join(config["fastqdir"], "%s_R1.barcoded.fastq" %(config["fastqprefix"])),
-            r3 = os.path.join(config["fastqdir"], "%s_R3.barcoded.fastq" %(config["fastqprefix"])),
+            r1 = os.path.join("Result/Tmp", "%s_R1.barcoded.fastq" %(config["fastqprefix"])),
+            r3 = os.path.join("Result/Tmp", "%s_R3.barcoded.fastq" %(config["fastqprefix"])),
         output:
             bam = temp("Result/minimap2/%s.sortedByPos.bam" %(config["outprefix"])),
         threads:
@@ -441,7 +458,7 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
     if config["whitelist"]:
         rule scatac_barcodecorrect:
             input:
-                r2 = os.path.join(config["fastqdir"], "%s_R2.fastq" %(config["fastqprefix"])),
+                r2 = os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"])),
                 whitelist = config["whitelist"],
             output:
                 bc_correct = "Result/minimap2/barcode_correct.txt",
@@ -456,7 +473,7 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
     else:
         rule scatac_barcodecorrect:
             input:
-                r2 = os.path.join(config["fastqdir"], "%s_R2.fastq" %(config["fastqprefix"])),
+                r2 = os.path.join("Result/Tmp", "%s_R2.fastq" %(config["fastqprefix"])),
             output:
                 bc_correct = "Result/minimap2/barcode_correct.txt",
                 bc_correct_uniq = "Result/minimap2/barcode_correct_uniq.txt",
@@ -537,15 +554,15 @@ if config["platform"] == "10x-genomics" or config["platform"] == "sci-ATAC-seq":
             bam = "Result/minimap2/%s.sortedByPos.CRadded.rmdp.bam" %(config["outprefix"]),
             metric = "Result/minimap2/%s.rmdp.txt" %(config["outprefix"]),
             fragbed = "Result/QC/%s_frag.bed" %(config["outprefix"]),
-            tmp = temp(directory("Result/Tmp"))
         params:
-            sam = "Result/minimap2/%s.sortedByPos.CRadded.rmdp.sample.sam" %(config["outprefix"])
+            sam = "Result/minimap2/%s.sortedByPos.CRadded.rmdp.sample.sam" %(config["outprefix"]),
+            tmp = "Result/Tmp",
         threads:
             int(config["cores"])-2
         benchmark:
             "Result/Benchmark/%s_Rmdp.benchmark" %(config["outprefix"])
         shell:
-            "picard MarkDuplicates INPUT={input.bam} OUTPUT={output.bam} METRICS_FILE={output.metric} TMP_DIR={output.tmp};"
+            "picard MarkDuplicates INPUT={input.bam} OUTPUT={output.bam} METRICS_FILE={output.metric} TMP_DIR={params.tmp};"
             "samtools view -@ {threads} -s 0.01 -o {params.sam} {input.bam};"
             "awk '{{if ($9>0) print $9}}' {params.sam} > {output.fragbed};"