Snakemake tabular config

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1















I'm using Snakemake with a tabular configuration. This table is a bunch of rows that I first take out of a very large sample overview. The resulting sample.tsv has a lot of columns. I read the samples file like this, somewhere in my Snakefile:



samples = pd.read_table('samples.tsv').set_index('samples', drop=False)


When I run snakemake:



snakemake --cluster-config cluster.json --cluster "qsub -l nodes={cluster.nodes}:ppn={cluster.ppn}" --jobs 256


I get the following error:




16:51 nlv24077@kiato ~/temp/test_snakemake > run_snakemake.sh
Building DAG of jobs...
MissingInputException in line 6 of /home/nlv24077/temp/test_snakemake/rseqc.smk:
Missing input files for rule bam_stat:
analyzed/I7_index.STAR.genome.sorted.bam



the strange thing is that I7_index is one of the column names in my samples table. Why is it using the column names as sample names?



Below I can show you part of the samples table (I can't show all data publicly):
enter image description here



Edit:



I was calling the samples like this:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples)
threads: 6
shell:
'''
# Run bcl2fastq
...


Whereas I should have used:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples['samples'])
threads: 6
shell:
'''
# Run bcl2fastq
...


Thanx JeeYem.










share|improve this question

























  • Can you show the relevant code related to this error? For eg., rule bam_stat.

    – JeeYem
    Jan 2 at 16:51






  • 1





    if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

    – JeeYem
    Jan 2 at 23:26













  • Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

    – Freek
    Jan 3 at 8:33











  • Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

    – Freek
    Jan 3 at 14:35








  • 1





    Please show relevant code. It's not easy to make sense of what exactly you are asking.

    – JeeYem
    Jan 3 at 16:01
















1















I'm using Snakemake with a tabular configuration. This table is a bunch of rows that I first take out of a very large sample overview. The resulting sample.tsv has a lot of columns. I read the samples file like this, somewhere in my Snakefile:



samples = pd.read_table('samples.tsv').set_index('samples', drop=False)


When I run snakemake:



snakemake --cluster-config cluster.json --cluster "qsub -l nodes={cluster.nodes}:ppn={cluster.ppn}" --jobs 256


I get the following error:




16:51 nlv24077@kiato ~/temp/test_snakemake > run_snakemake.sh
Building DAG of jobs...
MissingInputException in line 6 of /home/nlv24077/temp/test_snakemake/rseqc.smk:
Missing input files for rule bam_stat:
analyzed/I7_index.STAR.genome.sorted.bam



the strange thing is that I7_index is one of the column names in my samples table. Why is it using the column names as sample names?



Below I can show you part of the samples table (I can't show all data publicly):
enter image description here



Edit:



I was calling the samples like this:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples)
threads: 6
shell:
'''
# Run bcl2fastq
...


Whereas I should have used:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples['samples'])
threads: 6
shell:
'''
# Run bcl2fastq
...


Thanx JeeYem.










share|improve this question

























  • Can you show the relevant code related to this error? For eg., rule bam_stat.

    – JeeYem
    Jan 2 at 16:51






  • 1





    if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

    – JeeYem
    Jan 2 at 23:26













  • Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

    – Freek
    Jan 3 at 8:33











  • Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

    – Freek
    Jan 3 at 14:35








  • 1





    Please show relevant code. It's not easy to make sense of what exactly you are asking.

    – JeeYem
    Jan 3 at 16:01














1












1








1








I'm using Snakemake with a tabular configuration. This table is a bunch of rows that I first take out of a very large sample overview. The resulting sample.tsv has a lot of columns. I read the samples file like this, somewhere in my Snakefile:



samples = pd.read_table('samples.tsv').set_index('samples', drop=False)


When I run snakemake:



snakemake --cluster-config cluster.json --cluster "qsub -l nodes={cluster.nodes}:ppn={cluster.ppn}" --jobs 256


I get the following error:




16:51 nlv24077@kiato ~/temp/test_snakemake > run_snakemake.sh
Building DAG of jobs...
MissingInputException in line 6 of /home/nlv24077/temp/test_snakemake/rseqc.smk:
Missing input files for rule bam_stat:
analyzed/I7_index.STAR.genome.sorted.bam



the strange thing is that I7_index is one of the column names in my samples table. Why is it using the column names as sample names?



Below I can show you part of the samples table (I can't show all data publicly):
enter image description here



Edit:



I was calling the samples like this:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples)
threads: 6
shell:
'''
# Run bcl2fastq
...


Whereas I should have used:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples['samples'])
threads: 6
shell:
'''
# Run bcl2fastq
...


Thanx JeeYem.










share|improve this question
















I'm using Snakemake with a tabular configuration. This table is a bunch of rows that I first take out of a very large sample overview. The resulting sample.tsv has a lot of columns. I read the samples file like this, somewhere in my Snakefile:



samples = pd.read_table('samples.tsv').set_index('samples', drop=False)


When I run snakemake:



snakemake --cluster-config cluster.json --cluster "qsub -l nodes={cluster.nodes}:ppn={cluster.ppn}" --jobs 256


I get the following error:




16:51 nlv24077@kiato ~/temp/test_snakemake > run_snakemake.sh
Building DAG of jobs...
MissingInputException in line 6 of /home/nlv24077/temp/test_snakemake/rseqc.smk:
Missing input files for rule bam_stat:
analyzed/I7_index.STAR.genome.sorted.bam



the strange thing is that I7_index is one of the column names in my samples table. Why is it using the column names as sample names?



Below I can show you part of the samples table (I can't show all data publicly):
enter image description here



Edit:



I was calling the samples like this:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples)
threads: 6
shell:
'''
# Run bcl2fastq
...


Whereas I should have used:



rule bcl2fastq:
input:
config['bcl_dir']
output:
expand([os.path.join(fastq_dir, '{sample}_R1_001.fastq.gz'),
os.path.join(fastq_dir, '{sample}_R2_001.fastq.gz')],
sample=samples['samples'])
threads: 6
shell:
'''
# Run bcl2fastq
...


Thanx JeeYem.







bioinformatics snakemake






share|improve this question















share|improve this question













share|improve this question




share|improve this question








edited Jan 4 at 12:50







Freek

















asked Jan 2 at 16:00









FreekFreek

3881418




3881418













  • Can you show the relevant code related to this error? For eg., rule bam_stat.

    – JeeYem
    Jan 2 at 16:51






  • 1





    if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

    – JeeYem
    Jan 2 at 23:26













  • Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

    – Freek
    Jan 3 at 8:33











  • Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

    – Freek
    Jan 3 at 14:35








  • 1





    Please show relevant code. It's not easy to make sense of what exactly you are asking.

    – JeeYem
    Jan 3 at 16:01



















  • Can you show the relevant code related to this error? For eg., rule bam_stat.

    – JeeYem
    Jan 2 at 16:51






  • 1





    if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

    – JeeYem
    Jan 2 at 23:26













  • Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

    – Freek
    Jan 3 at 8:33











  • Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

    – Freek
    Jan 3 at 14:35








  • 1





    Please show relevant code. It's not easy to make sense of what exactly you are asking.

    – JeeYem
    Jan 3 at 16:01

















Can you show the relevant code related to this error? For eg., rule bam_stat.

– JeeYem
Jan 2 at 16:51





Can you show the relevant code related to this error? For eg., rule bam_stat.

– JeeYem
Jan 2 at 16:51




1




1





if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

– JeeYem
Jan 2 at 23:26







if samples column has the values of interest, are you sure you are using something like samples['samples'] (or samples.index.values to row indices) to obtain them?

– JeeYem
Jan 2 at 23:26















Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

– Freek
Jan 3 at 8:33





Oh, is that necessary? I thought the idea was that as long as the index is your samples, you are fine and you can even address the metadata just by column name. But I just need to really address a certain column? Then setting the samples as index is also not necessary. How then can I call a metadata column, for example when the samples have different read lengths defined in the sample table? Thanx for your swift reply by the way!

– Freek
Jan 3 at 8:33













Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

– Freek
Jan 3 at 14:35







Ok, so indeed that works, I misunderstood what the samples table was used for, it seems to be pretty simple (one can extract lists from it). Now I wonder how I can address other columns, is it using pure python? Like samples[samples['samples']==sample]['read_length] to get one value? I'll try that at least.

– Freek
Jan 3 at 14:35






1




1





Please show relevant code. It's not easy to make sense of what exactly you are asking.

– JeeYem
Jan 3 at 16:01





Please show relevant code. It's not easy to make sense of what exactly you are asking.

– JeeYem
Jan 3 at 16:01












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