snakemake-tutorial | head node of an HPC cluster running Slurm
kandi X-RAY | snakemake-tutorial Summary
kandi X-RAY | snakemake-tutorial Summary
For the purpose of the webinar we will be working on the head node of an HPC cluster running Slurm. This is the most likely infrastructure that fellow bioinformaticians already find themselves using on a regular basis. The execution of the Snakemake workflow will actually take place on the cluster head node with jobs being submitted to Slurm for queing and processing. From the head node, Snakemake will monitor the submitted jobs for their completion status and submit new jobs as dependent jobs complete sucessfully.
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QUESTION
I'm trying to practice writing workflows in snakemake.
The contents of my Snakefile:
...ANSWER
Answered 2020-Oct-28 at 08:52Looks like you want to run your Rscript twice per file, once for every value of col
. In this case, the rule needs to be called twice as well.
The use of expand
is also a bit too much here, in my opinion. expand
fills your wildcards with all possible values and returns a list of the resulting files. So the output for this rule would be all possible combinations between files
and cols
, which the simple script can not create in one run.
This is also the reason why file
can not be inferred from the output - it gets expanded there.
Instead, try writing your rule easier for just one file and column and expand on the resulting output, in a rule which needs this output as an input. If you generated the final output of your workflow, put it as input in a rule all
to tell the workflow what the ultimate goal is.
QUESTION
I am trying to execute the workflow of the Snakemake's official tutorial via Tibanna on AWS.
As instructed here,
- I have installed Tibanna and set up environment variables.
- Then I deployed Tibanna Unicorn to a folder snakemake-tutorial in a specific S3 bucket specific-bucket.
- I set up the default unicorn.
- As a last step, I run the following command:
ANSWER
Answered 2020-Sep-10 at 12:37I was able to solve this problem with the --precommand
flag.
QUESTION
I would like to know all necessary criteria required for snakemake to decide that a job needs to be executed, but I couldn't find them in their documentation. The best source I have found is in snakemake author's slides from 2016, which says:
...ANSWER
Answered 2020-Jun-17 at 03:51This page of their documentation has a link to the slides from 2019: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html. On the page 26 of the slides you may see the same set of rules: https://slides.com/johanneskoester/snakemake-tutorial#/25:
QUESTION
I'm a newbie using Snakemake and not an expert in Python neither so the answer might be quite obvious. Everything in my workflow worked fine in my tests until I tried to use glob_wildcards in order to turn all of my fastq.gz files from one directory (FASTQDIR) into fastqc files.
The samples names in the SAMPLES list are okay but I have an error saying that a string is expected instead of a list (I assume this is my SAMPLES list) and I don't really know where to act in my Snakefile in order to correct it. I understand that it is surely linked to my use of glob_wildcards but I don't understand where is the problem. Do you have an idea of how I can fix it ?
Here is my Snakefile code :
...ANSWER
Answered 2020-Mar-12 at 15:53You are not using wildcards here.
Your rule fastqc_generate_qc
takes as input ALL the fastq files and output ALL the fastqc files here.
One thing to remember in snakemake is: expand
produces a list of files. You don't want that here:
QUESTION
I am new to snakemake and have an issue with the following code that should take 9 fastq files one after another and apply fastqc.
smp should take the values:
UG1_S12 UG2_S13 UG3_S14 UR1_S1 UR2_S2 UR3_S3 UY1_S6 UY2_S7 UY3_S8
Which works when I run
...ANSWER
Answered 2018-Oct-24 at 15:21If you want to use the wildcards in the shell command, you have to use {wildcards.smp}
.
What is probably happening is that {smp}
in the shell command takes the value of the last iteration of the for loop above. So change:
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