Mixing
Recursive input calling in Snakemake rule
I am writing rule to process some data:
data in directory will be something like:
myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...
rule trim_data:
input:"{dataset}/{sample}.trim_{r}P"
output:"{dataset}/{sample}.{r}.fastq"
params:
length=14
shell:
"""
reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"
"""
I have this error:
WorkflowError:
RecursionError: maximum recursion depth exceeded
If building the DAG exceeds the recursion limit
myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....
Why it run in recursive way if the output different from the input? and how I can fix it?
snakemake
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
add a comment |
I am writing rule to process some data:
data in directory will be something like:
myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...
rule trim_data:
input:"{dataset}/{sample}.trim_{r}P"
output:"{dataset}/{sample}.{r}.fastq"
params:
length=14
shell:
"""
reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"
"""
I have this error:
WorkflowError:
RecursionError: maximum recursion depth exceeded
If building the DAG exceeds the recursion limit
myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....
Why it run in recursive way if the output different from the input? and how I can fix it?
snakemake
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
add a comment |
I am writing rule to process some data:
data in directory will be something like:
myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...
rule trim_data:
input:"{dataset}/{sample}.trim_{r}P"
output:"{dataset}/{sample}.{r}.fastq"
params:
length=14
shell:
"""
reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"
"""
I have this error:
WorkflowError:
RecursionError: maximum recursion depth exceeded
If building the DAG exceeds the recursion limit
myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....
Why it run in recursive way if the output different from the input? and how I can fix it?
snakemake
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
I am writing rule to process some data:
data in directory will be something like:
myfirst.trim_1P, myfirst.trim_2P, mysecond.trim_1P, mysecond.trim_2P,...
rule trim_data:
input:"{dataset}/{sample}.trim_{r}P"
output:"{dataset}/{sample}.{r}.fastq"
params:
length=14
shell:
"""
reformat.sh forcetrimleft="{params.length}" in="{input}" out="{output}"
"""
I have this error:
WorkflowError:
RecursionError: maximum recursion depth exceeded
If building the DAG exceeds the recursion limit
myDir/myfirst.1.trimed.1.trimed.2.trimed.2.trimed.2....
Why it run in recursive way if the output different from the input? and how I can fix it?
snakemake
snakemake
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
edited Nov 22 '18 at 18:22
Medhat
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
asked Nov 21 '18 at 21:50
MedhatMedhat
938820
938820
add a comment |
add a comment |
1 Answer
1
active
oldest
votes
This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:
wildcard_constraints:
dataset= '|'.join([re.escape(x) for x in DATASET]),
sample= '|'.join([re.escape(x) for x in SAMPLE]),
r= '|'.join([re.escape(x) for x in R]),
Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like thisrule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat
Nov 26 '18 at 20:23
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:
wildcard_constraints:
dataset= '|'.join([re.escape(x) for x in DATASET]),
sample= '|'.join([re.escape(x) for x in SAMPLE]),
r= '|'.join([re.escape(x) for x in R]),
Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like thisrule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat
Nov 26 '18 at 20:23
add a comment |
This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:
wildcard_constraints:
dataset= '|'.join([re.escape(x) for x in DATASET]),
sample= '|'.join([re.escape(x) for x in SAMPLE]),
r= '|'.join([re.escape(x) for x in R]),
Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like thisrule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat
Nov 26 '18 at 20:23
add a comment |
This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:
wildcard_constraints:
dataset= '|'.join([re.escape(x) for x in DATASET]),
sample= '|'.join([re.escape(x) for x in SAMPLE]),
r= '|'.join([re.escape(x) for x in R]),
Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
This is a wild guess... Maybe the wildcards capture more then they should since they are interpreted as regular expression. If {dataset}, {sample} and {r} take a defined list of values, try constraining their scope with:
wildcard_constraints:
dataset= '|'.join([re.escape(x) for x in DATASET]),
sample= '|'.join([re.escape(x) for x in SAMPLE]),
r= '|'.join([re.escape(x) for x in R]),
Where DATASET, SAMPLE and R are lists of values (e.g. R= ['1', '2'])
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
answered Nov 22 '18 at 10:07
darioberdariober
1,0361221
1,0361221
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like thisrule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat
Nov 26 '18 at 20:23
add a comment |
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like thisrule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)
– Medhat
Nov 26 '18 at 20:23
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
Thanks, this could be the case I will test it and give feedback.
– Medhat
Nov 22 '18 at 18:33
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
unfortunately, it did not work. I will try to figure something else, Thanks.
– Medhat
Nov 26 '18 at 16:00
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this
rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)– Medhat
Nov 26 '18 at 20:23
So the error was in another downstream rule that could cause this recursion I fixed it and add some constraints on the name like this
rule bam2fastq: input: datain="{dataset}/{sample}.{filter, ^[0-9]}.bam" output: dataout="{dataset}/{sample}.{filter}.reads.fastq" run: shell(""" bedtools bamtofastq -i "{input.datain}" -fq "{output.dataout}" """)– Medhat
Nov 26 '18 at 20:23
add a comment |
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