added rule heatmap

ATAC-seq_pipeline/Snakefile

@@ -64,14 +64,14 @@ NARROWPEAK          =       expand(RESULT_DIR     + "macs2/{samples}_peaks.narro
 COVERAGE_TRACK      =       expand(RESULT_DIR     + "bamCoverage/{samples}.bw", samples = SAMPLES),
 BIGWIGSUMMARY       =        RESULT_DIR     + "bigwigsummary/multiBigwigSummary.npz",
 PCAPLOT             =        RESULT_DIR     + "PCA/PCA_PLOT.pdf"
+HEATMAP             =       RESULT_DIR + "heatmap/heatmap_reference_point_genes.pdf"
+
+
+container: "docker://continuumio/miniconda3:4.4.10"
 
 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",
         FORWARD_READS,
         REVERSE_READS,
         TRIMMED_FASTQC,
@@ -85,13 +85,17 @@ rule all:
         #PCAPLOT,
         #SORTED_INDEXED,
         #NARROWPEAK,
-        HMMRATAC,
+        #HMMRATAC,
+        HEATMAP
 
     message : "Analysis is complete!"
+    log:
+        "log/rule_all.log"
     shell:""
 
 ################## INCLUDE RULES ##################
 include: "rules/external_data.smk"
 include: "rules/pre-processing.smk"
 include: "rules/macs2.smk"
+include: "rules/deeptools.smk"
 include: "rules/hmmratac.smk"

ATAC-seq_pipeline/config.yaml

@@ -52,3 +52,7 @@ bamCoverage:
   effectiveGenomeSize: "2652783500"
   normalization: "RPKM"
   binSize: "1000"
+
+# computeMatrix
+ComputeMatrix:
+  GTF: "gencode.vM25.annotation.gtf"  

ATAC-seq_pipeline/rules/deeptools.smk

@@ -61,3 +61,26 @@ rule PCA:
         -o {output} \
         2>{log}
         """
+rule ComputeMatrix:
+    input:
+        lambda wildcards: expand(RESULT_DIR + "bamCoverage/{sample}.bw", sample = SAMPLES)
+    output:
+        RESULT_DIR + "computematrix/ComputeMatrix.gz"
+    log:
+        RESULT_DIR + "logs/computematrix/matrix.log"
+    conda:
+        "envs/deeptools.yaml"
+    params:
+        GTF = str(config['ComputeMatrix']['GTF'])
+    shell:
+        "computeMatrix reference-point -S {input} -R {params.GTF} -o {output} -a 3000 -b 3000 2>{log}"
+
+rule plotHeatmap:
+    input:
+        RESULT_DIR + "computematrix/ComputeMatrix.gz"
+    output:
+        RESULT_DIR + "heatmap/heatmap_reference_point_genes.pdf"
+    conda:
+        "envs/deeptools.yaml"
+    shell:
+        "plotHeatmap -m {input} -o {output}"