Skip to content
GitLab
Unverified Commit bab1a3b4 authored by Jihed Chouaref's avatar Jihed Chouaref Committed by GitHub
Browse files

Update and rename snakefile to Snakefile

parent d3011c41
Hide whitespace changes
Inline Side-by-side
ATAC-seq_pipeline/snakefile → ATAC-seq_pipeline/Snakefile
View file @ bab1a3b4
......@@ -42,24 +42,27 @@ wildcard_constraints:
################## DESIRED OUTPUT ##################
FASTQC = expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html",numbers = ['8','12','4_3','4_1'], R=['R1', 'R2']),
FORWARD_READS = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
REVERSE_READS = expand(WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz", samples = SAMPLES),
TRIMMED_FASTQC = expand(RESULT_DIR + "trimmed_fastqc/{samples}_{direction}_fastqc.html", samples = SAMPLES, direction=['forward', 'reverse']),
MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
UNMAPPED = expand([WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)], samples = SAMPLES),
MAP_SORTED = expand(WORKING_DIR + "sort/{samples}.sorted.bam", samples = SAMPLES),
DEDUP = expand(WORKING_DIR + "dedup/{samples}.dedup.bam", samples = SAMPLES),
STATS = expand(WORKING_DIR + "dedup/{samples}.dedup.stats", samples = SAMPLES),
SORTED_INDEXED = expand(WORKING_DIR + "index/{samples}.sorted.bam.bai", samples = SAMPLES),
GENOME_INFO = expand(WORKING_DIR + "genome_info/{samples}.genome.info", samples = SAMPLES),
GAPPED_PEAK = expand(RESULT_DIR + "peaks/{samples}_peaks.gappedPeak", samples = SAMPLES),
NAME_LOG = expand(RESULT_DIR + "peaks/{samples}.log", samples = SAMPLES),
NARROWPEAK = expand(RESULT_DIR + "macs2/{samples}_peaks.narrowPeak", samples = SAMPLES),
COVERAGE_TRACK = expand(WORKING_DIR + "bamCoverage/{samples}.bw", samples = SAMPLES),
BIGWIGSUMMARY = expand(WORKING_DIR + "bigwigsummary/{samples}.npz", samples = SAMPLES),
PCAPLOT = expand(RESULT_DIR + "PCA/{samples}_pca.png", samples = SAMPLES)
# Here we define the outputs of rules we want the pipeline to produce.
# The varialble defined here is then used in the `rule all`.
# Fastqc rule need to be modified to accept any sample
FASTQC = expand(RESULT_DIR + "fastqc/sample_{numbers}_{R}_fastqc.html",numbers = ['8','12','4_3','4_1'], R=['R1', 'R2']),
FORWARD_READS = expand(WORKING_DIR + "trimmed/{samples}_forward.fastq.gz", samples = SAMPLES),
REVERSE_READS = expand(WORKING_DIR + "trimmed/{samples}_reverse.fastq.gz", samples = SAMPLES),
TRIMMED_FASTQC = expand(RESULT_DIR + "trimmed_fastqc/{samples}_{direction}_fastqc.html", samples = SAMPLES, direction=['forward', 'reverse']),
MAPPED = expand(WORKING_DIR + "mapped/{samples}.bam", samples = SAMPLES),
UNMAPPED = expand([WORKING_DIR + "unmapped/{samples}.fq." + str(i) +".gz" for i in range(1,2)], samples = SAMPLES),
MAP_SORTED = expand(WORKING_DIR + "sort/{samples}.sorted.bam", samples = SAMPLES),
DEDUP = expand(WORKING_DIR + "dedup/{samples}.dedup.bam", samples = SAMPLES),
STATS = expand(WORKING_DIR + "dedup/{samples}.dedup.stats", samples = SAMPLES),
SORTED_INDEXED = expand(WORKING_DIR + "sort/{samples}.sorted.bam.bai", samples = SAMPLES),
GENOME_INFO = expand(WORKING_DIR + "genome_info/{samples}.genome.info", samples = SAMPLES),
GAPPED_PEAK = expand(RESULT_DIR + "peaks/{samples}_peaks.gappedPeak", samples = SAMPLES),
NAME_LOG = expand(RESULT_DIR + "peaks/{samples}.log", samples = SAMPLES),
NARROWPEAK = expand(RESULT_DIR + "macs2/{samples}_peaks.narrowPeak", samples = SAMPLES),
COVERAGE_TRACK = expand(RESULT_DIR + "bamCoverage/{samples}.bw", samples = SAMPLES),
BIGWIGSUMMARY = RESULT_DIR + "bigwigsummary/multiBigwigSummary.npz",
PCAPLOT = RESULT_DIR + "PCA/PCA_PLOT.pdf"
rule all:
input:
......@@ -79,8 +82,8 @@ rule all:
COVERAGE_TRACK,
BIGWIGSUMMARY,
PCAPLOT,
#SORTED_INDEXED,
#NARROWPEAK,
SORTED_INDEXED,
NARROWPEAK,
#GENOME_INFO,
#GAPPED_PEAK,
#NAME_LOG
......@@ -204,15 +207,19 @@ rule mapping:
rule sort:
input:
mapped = WORKING_DIR + "mapped/{samples}.bam"
mapped = WORKING_DIR + "mapped/{samples}.bam"
output:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
sorted = WORKING_DIR + "sort/{samples}.sorted.bam",
bai = WORKING_DIR + "sort/{samples}.sorted.bam.bai"
conda:
"envs/samtools_bowtie.yaml"
log:
RESULT_DIR + "logs/sort/{samples}.log"
shell:
"samtools sort {input} -o {output} &>{log}"
"""
samtools sort {input} -o {output.sorted} &>{log}
samtools index {output.sorted}
"""
rule deduplication:
input:
......@@ -229,17 +236,17 @@ rule deduplication:
picard MarkDuplicates -I {input} -O {output.dedup} -M {output.stats} 2>{log}
"""
rule index:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
output:
map_sorted_indexed = WORKING_DIR + "sort/{samples}.sorted.bam.bai"
conda:
"envs/samtools_bowtie.yaml"
log:
RESULT_DIR + "logs/index/{samples}.log"
shell:
"samtools index {input} {output} &>{log}"
# #rule index:
# #input:
# map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
# output:
# map_sorted_indexed = WORKING_DIR + "sort/{samples}.sorted.bam.bai"
# conda:
# "envs/samtools_bowtie.yaml"
# log:
# RESULT_DIR + "logs/index/{samples}.log"
# shell:
# "samtools index {input} {output} &>{log}"
rule get_genome_info:
input:
......@@ -298,39 +305,44 @@ rule bamCoverage:
input:
map_sorted = WORKING_DIR + "sort/{samples}.sorted.bam"
output:
coverage_track = WORKING_DIR + "bamCoverage/{samples}.bw"
coverage_track = RESULT_DIR + "bamCoverage/{samples}.bw"
params:
effectiveGenomeSize = str(config['bamCoverage']['effectiveGenomeSize']),
normalization = str(config['bamCoverage']['normalization'])
effectiveGenomeSize = str(config['bamCoverage']['effectiveGenomeSize']),
normalization = str(config['bamCoverage']['normalization']),
binSize = str(config['bamCoverage']['binSize'])
log:
RESULT_DIR + "logs/bamCoverage/{samples}.bw.log"
conda:
"envs/deeptools.yaml"
shell:
"bamCoverage -b {input} --effectiveGenomeSize {params.effectiveGenomeSize} --normalizeUsing {params.normalization} --ignoreDuplicates -o {output}"
"bamCoverage -b {input} --effectiveGenomeSize {params.effectiveGenomeSize} --normalizeUsing {params.normalization} --ignoreDuplicates -o {output} --binSize {params.binSize}"
#bdg: create bedgraph output files
#format=BAMPE: only use properly-paired read alignments
# rule multibigwigSummary need to be expanded to use more than 1 bigwig file
# Right now the file only use 1 file, which is not useful for a comparison
rule multibigwigSummary:
input:
coverage_track = WORKING_DIR + "bamCoverage/{samples}.bw"
lambda wildcards: expand(RESULT_DIR + "bamCoverage/{sample}.bw", sample = SAMPLES)
output:
bigwigsummary = WORKING_DIR + "bigwigsummary/{samples}.npz"
bigwigsummary = RESULT_DIR + "bigwigsummary/multiBigwigSummary.npz"
log:
RESULT_DIR + "logs/bigwigsummary/{samples}.bw.log"
RESULT_DIR + "logs/bigwigsummary/multiBigwigSummary.log"
conda:
"envs/deeptools.yaml"
shell:
"multiBigwigSummary bins -b {input} -o {output}"
"multiBigwigSummary bins -b {input} -o {output} "
#2>{log}
# PlotPCA does not work with a bigwigsummary made of only one sample
rule PCA:
input:
bigwigsummary = WORKING_DIR + "bigwigsummary/{samples}.npz"
bigwigsummary = RESULT_DIR + "bigwigsummary/multiBigwigSummary.npz"
output:
PCAplot = RESULT_DIR + "PCA/{samples}_pca.png"
PCAplot = RESULT_DIR + "PCA/PCA_PLOT.pdf"
log:
RESULT_DIR + "logs/bigwigsummary/{samples}_pca.png.log"
RESULT_DIR + "logs/bigwigsummary/PCA_PLOT.log"
conda:
"envs/deeptools.yaml"
shell:
"plotPCA -in {input} -o {output}"
"plotPCA -in {input} -o {output} 2>{log}"
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment