Commit 63c28e21 authored by JihedC's avatar JihedC
Browse files

added rule heatmap

parent 77741dda
......@@ -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"
......@@ -52,3 +52,7 @@ bamCoverage:
effectiveGenomeSize: "2652783500"
normalization: "RPKM"
binSize: "1000"
# computeMatrix
ComputeMatrix:
GTF: "gencode.vM25.annotation.gtf"
......@@ -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}"
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