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|
cores_choices = [1, 2, 4]
chromap = expand(
"output/result.chromap.{cores}.pairs",
cores=cores_choices,
)
juicer = expand(
"output/result.juicer.{cores}.pairs",
cores=cores_choices,
)
hicexplorer = expand(
"output/result.hicexplorer.{cores}.cool",
cores=cores_choices,
)
fanc_bwa = expand(
"output/result.fanc_bwa.{cores}.pairs",
cores=cores_choices,
)
fanc_bowtie = expand(
"output/result.fanc_bowtie2.{cores}.pairs",
cores=cores_choices,
)
hicpro = expand(
"output/result.hicpro.{cores}.pairs",
cores=cores_choices,
)
tadbit = expand(
"output/result.tadbit.{cores}.reads",
cores=cores_choices,
)
tadbit_bowtie = expand(
"output/result.tadbit_bowtie2.{cores}.reads",
cores=cores_choices,
)
pairtools = expand(
"output/result.pairtools.{cores}.pairs",
cores=cores_choices,
)
pairtools_bwamem2 = expand(
"output/result.pairtools_bwamem2.{cores}.pairs",
cores=cores_choices,
)
# mapping only:
bowtie = expand(
"output/result.bowtie.{cores}.sam",
cores=cores_choices,
)
bwamem = expand(
"output/result.bwamem.{cores}.sam",
cores=cores_choices,
)
bwamem2 = expand(
"output/result.bwamem2.{cores}.sam",
cores=cores_choices,
)
rule all:
input:
lambda wildcards: tadbit + tadbit_bowtie + bowtie + bwamem2 + pairtools + pairtools_bwamem2 + chromap + hicpro + fanc_bowtie + fanc_bwa + hicexplorer
# + bowtie + bwamem + bwamem2
# + juicer
# + pairtools + pairtools_bwamem2 + chromap + hicpro + fanc_bowtie + fanc_bwa + hicexplorer
# hicexplorer # heavy because it creates coolers
# juicer # run separately with the number of cores equal to tested, b/c multiplw juicers cannot be run with the same path
rule test:
input:
fastq1="data/SRR6107789_1.fastq.gz",
fastq2="data/SRR6107789_2.fastq.gz",
genomefile="data/hg38/hg38.fa",
chromsizes="data/hg38/hg38.fa.sizes",
genome_index_bwa="data/hg38/index/bwa/hg38.fa",
genome_index_chromap="data/hg38/index/chromap/hg38",
genome_index_bwamem2="data/hg38/index/bwa-mem2/hg38",
genome_index_bowtie2="data/hg38/index/bowtie2/hg38",
genome_index_gem="data/hg38/index/gem/hg38.gem",
genome_rsites="data/hg38/hg38.DpnII.bed",
threads: lambda wildcards: int(wildcards.cores),
output:
file="output/result.{mode}.{cores}.{format}",
benchmark:
repeat(
"benchmarks/result.{mode}.{cores}.{format}.benchmark",
5,
)
run:
if wildcards.mode == "pairtools_bwamem2":
shell("""
soft/bwa-mem2/bwa-mem2 mem -t {wildcards.cores} -SP {input.genome_index_bwamem2} {input.fastq1} {input.fastq2} | \
soft/pairtools1.0.2/bin/pairtools parse --nproc-in {wildcards.cores} --nproc-out {wildcards.cores} --drop-sam --drop-seq -c {input.chromsizes} | \
soft/pairtools1.0.2/bin/pairtools sort --nproc {wildcards.cores} | \
soft/pairtools1.0.2/bin/pairtools dedup -p {wildcards.cores} --chunksize 1000000 \
-o {output.file}
""")
elif wildcards.mode == "pairtools":
shell("""
soft/pairtools1.0.2/bin/bwa mem -t {wildcards.cores} -SP {input.genome_index_bwa} {input.fastq1} {input.fastq2} | \
soft/pairtools1.0.2/bin/pairtools parse --nproc-in {wildcards.cores} --nproc-out {wildcards.cores} --drop-sam --drop-seq -c {input.chromsizes} | \
soft/pairtools1.0.2/bin/pairtools sort --nproc {wildcards.cores} | \
soft/pairtools1.0.2/bin/pairtools dedup -p {wildcards.cores} --chunksize 1000000 \
-o {output.file}
""")
elif wildcards.mode == "chromap":
shell("""
soft/chromap/bin/chromap --preset hic \
-t {wildcards.cores} -x {input.genome_index_chromap} -r {input.genomefile} \
-1 {input.fastq1} -2 {input.fastq2} -o {output.file}
""")
elif wildcards.mode == "fanc_bwa":
shell("""
TMP_FILE1=$(mktemp -u output/tmp.XXXXXXXX.bam)
TMP_FILE2=$(mktemp -u output/tmp.XXXXXXXX.bam)
soft/fanc/bin/fanc map -t {wildcards.cores} {input.fastq1} {input.genome_index_bwa} $TMP_FILE1
samtools sort -n -@ {wildcards.cores} $TMP_FILE1 -o $TMP_FILE1.sorted.bam
soft/fanc/bin/fanc map -t {wildcards.cores} {input.fastq2} {input.genome_index_bwa} $TMP_FILE2
samtools sort -n -@ {wildcards.cores} $TMP_FILE2 -o $TMP_FILE2.sorted.bam
soft/fanc/bin/fanc pairs -f -g {input.genome_rsites} $TMP_FILE1.sorted.bam $TMP_FILE2.sorted.bam {output.file}
rm $TMP_FILE1 $TMP_FILE2 $TMP_FILE1.sorted.bam $TMP_FILE2.sorted.bam
""")
elif wildcards.mode == "fanc_bowtie2":
shell("""
TMP_FILE1=$(mktemp -u output/tmp.XXXXXXXX.bam)
TMP_FILE2=$(mktemp -u output/tmp.XXXXXXXX.bam)
soft/fanc/bin/fanc map -t {wildcards.cores} {input.fastq1} {input.genome_index_bowtie2} $TMP_FILE1
samtools sort -n -@ {wildcards.cores} $TMP_FILE1 -o $TMP_FILE1.sorted.bam
soft/fanc/bin/fanc map -t {wildcards.cores} {input.fastq2} {input.genome_index_bowtie2} $TMP_FILE2
samtools sort -n -@ {wildcards.cores} $TMP_FILE2 -o $TMP_FILE2.sorted.bam
soft/fanc/bin/fanc pairs -f -g {input.genome_rsites} $TMP_FILE1.sorted.bam $TMP_FILE2.sorted.bam {output.file}
rm $TMP_FILE1 $TMP_FILE2 $TMP_FILE1.sorted.bam $TMP_FILE2.sorted.bam
""")
elif wildcards.mode == "hicpro":
shell("""
cd soft/HiC-Pro_env/HiC-Pro/
mkdir -p output
TMP_DIR=$(mktemp -d -u output/tmp.XXXXXXXX)
TMP_CONFIG=$(mktemp -u output/tmp.XXXXXXXX.config)
cp config-hicpro.txt $TMP_CONFIG
sed -i 's/N_CPU = 4/N_CPU = {wildcards.cores}/' $TMP_CONFIG
bin/HiC-Pro -i rawdata/ -o $TMP_DIR -c $TMP_CONFIG
# Cleanup:
cp $TMP_DIR/hic_results/data/sample1/sample1.allValidPairs ../../../{output.file}
rm -r $TMP_DIR; rm $TMP_CONFIG
""")
elif wildcards.mode == "juicer":
# Note that this process is not guaranteed to work well in parallel mode;
# recommended to run separately
shell("""
soft/juicer-1.6/CPU/juicer.sh -g hg38 -d data/4juicer/ -s DpnII -S early \
-p {input.chromsizes} -y {input.genome_rsites} -z {input.genome_index_bwa} -t {wildcards.cores} -D soft/juicer-1.6/CPU
# Cleanup:
mv data/4juicer/aligned/merged_nodups.txt {output.file}
rm -rf data/4juicer/aligned; rm -rf data/4juicer/splits/[^S]*
""")
elif wildcards.mode == "hicexplorer":
shell("""
TMP_DIR=$(mktemp -d -u output/tmp.XXXXXXXX)
soft/hicexplorer/bin/hicBuildMatrix --samFiles \
<(bwa mem -A1 -B4 -E50 -L0 {input.genome_index_bwa} -t {wildcards.cores} {input.fastq1} | samtools view -@ {wildcards.cores} -Shb -) \
<(bwa mem -A1 -B4 -E50 -L0 {input.genome_index_bwa} -t {wildcards.cores} {input.fastq2} | samtools view -@ {wildcards.cores} -Shb -) \
--restrictionSequence GATC \
--danglingSequence GATC \
--restrictionCutFile {input.genome_rsites} \
--threads {wildcards.cores} \
--inputBufferSize 1000000 \
--QCfolder $TMP_DIR \
-o {output.file}
# Cleanup:
rm -r $TMP_DIR
""")
elif wildcards.mode == "tadbit":
shell("""
TMP_DIR=$(mktemp -d -u tadbit_output/tmp.XXXXXXXX)
soft/tadbit/bin/tadbit map $TMP_DIR -C {wildcards.cores} --mapper_binary soft/tadbit/bin/gem-mapper --fastq {input.fastq1} --read 1 --index {input.genome_index_gem} --renz DpnII || true
soft/tadbit/bin/tadbit map $TMP_DIR -C {wildcards.cores} --mapper_binary soft/tadbit/bin/gem-mapper --fastq {input.fastq2} --read 2 --index {input.genome_index_gem} --renz DpnII || true
soft/tadbit/bin/tadbit parse $TMP_DIR --genome data/hg38/hg38.fa || true
soft/tadbit/bin/tadbit filter $TMP_DIR -C {wildcards.cores} --format mid || true
mv $TMP_DIR/03_filtered_reads/valid_r1-r2_intersection_*.tsv {output.file}
rm -r $TMP_DIR
""")
elif wildcards.mode == "tadbit_bowtie2":
shell("""
TMP_DIR=$(mktemp -d -u tadbit_output/tmp.XXXXXXXX)
soft/tadbit/bin/tadbit map $TMP_DIR -C {wildcards.cores} --mapper bowtie2 --mapper_binary soft/tadbit/bin/bowtie2 --fastq {input.fastq1} --read 1 --index {input.genome_index_bowtie2} --renz DpnII || true
soft/tadbit/bin/tadbit map $TMP_DIR -C {wildcards.cores} --mapper bowtie2 --mapper_binary soft/tadbit/bin/bowtie2 --fastq {input.fastq2} --read 2 --index {input.genome_index_bowtie2} --renz DpnII || true
soft/tadbit/bin/tadbit parse $TMP_DIR --genome data/hg38/hg38.fa || true
soft/tadbit/bin/tadbit filter $TMP_DIR -C {wildcards.cores} --format mid || true
mv $TMP_DIR/03_filtered_reads/valid_r1-r2_intersection_*.tsv {output.file}
rm -r $TMP_DIR
""")
elif wildcards.mode == "bowtie":
shell("""
soft/tadbit/bin/bowtie2 -p 4 -x {input.genome_index_bowtie2} -1 {input.fastq1} -2 {input.fastq2} -S {output.file}
""")
elif wildcards.mode == "bwamem":
shell("""
soft/pairtools0.3.0/bin/bwa mem -t 4 -SP {input.genome_index_bwa} {input.fastq1} {input.fastq2} > {output.file}
""")
elif wildcards.mode == "bwamem2":
shell("""
soft/bwa-mem2/bwa-mem2 mem -t 4 -SP {input.genome_index_bwamem2} {input.fastq1} {input.fastq2} > {output.file}
""")
|
