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adding no input control functionality #25

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Nov 10, 2023
Merged

adding no input control functionality #25

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59 changes: 31 additions & 28 deletions workflow/rules/peakcall.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,24 @@ def get_input_bam(wildcards):
# Runs in ChIP-only mode
return []

def get_control_input(wildcards):
if paired_end and chip2input[wildcards.name] != "":
i = [
join(workpath, bam_dir, "{0}.Q5DD.bam".format(chip2input[wildcards.name]))
]
return i
elif paired_end and chip2input[wildcards.name] == "":
i = []
return i
elif not paired_end and chip2input[wildcards.name] != "":
i = [
join(workpath, bam_dir, "{0}.Q5DD_tagAlign.gz".format(chip2input[wildcards.name]))
]
return i
else:
i = []
return i

rule sortByRead:
"""
Bam files(extension: sorted.bam) need to be sorted by read name
Expand Down Expand Up @@ -78,12 +96,7 @@ rule MACS2_narrow:
if paired_end else join(workpath,bam_dir, w.name+".Q5DD_tagAlign.gz"),
txt = lambda w: join(workpath,bam_dir, ppqt_dir, w.name+".Q5DD.ppqt.txt") \
if paired_end else join(workpath,bam_dir, ppqt_dir, w.name+".Q5DD_tagAlign.ppqt.txt"),
c_option_pe = provided( lambda w: "{0}.Q5DD.bam".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end == True),
c_option_se = provided(lambda w: "{0}.Q5DD_tagAlign.gz".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end == False) # Building optional argument for paired input option, input: '-c /path/to/input.Q5DD.bam', No input: ''
c_option = get_control_input
output:
join(workpath,macsN_dir,"{name}","{name}_peaks.narrowPeak"),
params:
Expand All @@ -96,7 +109,7 @@ rule MACS2_narrow:
module load {params.macsver};
if [ '{params.paired_end}' == True ]; then
macs2 callpeak \\
-t {input.chip} {params.flag} {input.c_option_pe} \\
-t {input.chip} {params.flag} {input.c_option} \\
-g {params.gsize} \\
-n {wildcards.name} \\
--outdir {workpath}/{macsN_dir}/{wildcards.name} \\
Expand All @@ -106,7 +119,7 @@ rule MACS2_narrow:
else
ppqt_len=$(awk '{{print $1}}' {input.txt})
macs2 callpeak \\
-t {input.chip} {params.flag} {input.c_option_se} \\
-t {input.chip} {params.flag} {input.c_option} \\
-g {params.gsize} \\
-n {wildcards.name} \\
--outdir {workpath}/{macsN_dir}/{wildcards.name} \\
Expand All @@ -123,12 +136,7 @@ rule MACS2_broad:
if paired_end else join(workpath,bam_dir, w.name+".Q5DD_tagAlign.gz"),
txt = lambda w: join(workpath,bam_dir, ppqt_dir, w.name+".Q5DD.ppqt.txt") \
if paired_end else join(workpath,bam_dir, ppqt_dir, w.name+".Q5DD_tagAlign.ppqt.txt"),
c_option_pe = provided(lambda w: "{0}.Q5DD.bam".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end == True),
c_option_se = provided(lambda w: "{0}.Q5DD_tagAlign.gz".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end ==False)
c_option = get_control_input
output:
join(workpath,macsB_dir,"{name}","{name}_peaks.broadPeak"),
params:
Expand All @@ -141,7 +149,7 @@ rule MACS2_broad:
module load {params.macsver};
if [ '{params.paired_end}' == True ]; then
macs2 callpeak \\
-t {input.chip} {params.flag} {input.c_option_pe} \\
-t {input.chip} {params.flag} {input.c_option} \\
-g {params.gsize} \\
-n {wildcards.name} \\
--outdir {workpath}/{macsB_dir}/{wildcards.name} \\
Expand All @@ -152,7 +160,7 @@ rule MACS2_broad:
else
ppqt_len=$(awk '{{print $1}}' {input.txt})
macs2 callpeak \\
-t {input.chip} {params.flag} {input.c_option_se} \\
-t {input.chip} {params.flag} {input.c_option} \\
-g {params.gsize} \\
-n {wildcards.name} \\
--outdir {workpath}/{macsB_dir}/{wildcards.name} \\
Expand All @@ -170,12 +178,7 @@ rule SICER:
if paired_end else join(workpath,bam_dir, w.name+".Q5DD_tagAlign.gz"),
fragLen =lambda w: join(workpath,bam_dir, ppqt_dir, w.name+".Q5DD_tagAlign.ppqt.txt") if \
not paired_end else join(workpath,"QC", w.name+".Q5DD.insert_size_metrics.txt"),
c_option_pe = provided(lambda w: "{0}.Q5DD.bam".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end==True),
c_option_se = provided(lambda w: "{0}.Q5DD_tagAlign.gz".format(
join(workpath, bam_dir, chip2input[w.name])
) if chip2input[w.name] else "", paired_end==False)
c_option = get_control_input
output:
bed = join(workpath,sicer_dir,"{name}","{name}_broadpeaks.bed"),
params:
Expand Down Expand Up @@ -203,16 +206,16 @@ rule SICER:
mean_insert_size=$(awk '{{print $1}}' {input.fragLen})
fi
echo "printing out value of mean-insert-size ${{mean_insert_size}}"
a={input.c_option_se}
echo "Printing input.c_option_se ${{a}}"
a={input.c_option}
echo "Printing input.c_option ${{a}}"
if [ '{params.paired_end}' == True ]; then
echo "praired-end with input"
if [ -f "{input.c_option_pe}" ];
if [ -f "{input.c_option}" ];
then
echo "praired-end with input"
sicer \\
-t {input.chip} \\
-c {input.c_option_pe} \\
-c {input.c_option} \\
-s {params.genomever} \\
-rt 100 \\
-w 300 \\
Expand Down Expand Up @@ -242,13 +245,13 @@ rule SICER:
mv ${{tmp}}/{params.name}.Q5DD-W300-G600.scoreisland {params.sicer_dir}
fi
else
if [ -f "{input.c_option_se}" ];
if [ -f "{input.c_option}" ];
then
echo "single-end with input"
cp {input.chip} ${{tmp}}/chip.bed.gz; gzip -d ${{tmp}}/chip.bed.gz;
awk 'BEGIN{{FS=OFS="\\t"}} {{gsub(/\./, 0, $5)}} 1' ${{tmp}}/chip.bed > ${{tmp}}/{params.name}.bed;

cp {input.c_option_se} ${{tmp}}/input.bed.gz; gzip -d ${{tmp}}/input.bed.gz;
cp {input.c_option} ${{tmp}}/input.bed.gz; gzip -d ${{tmp}}/input.bed.gz;
awk 'BEGIN{{FS=OFS="\\t"}} {{gsub(/\./, 0, $5)}} 1' ${{tmp}}/input.bed > ${{tmp}}/inputV2.bed;

sicer \\
Expand Down
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