Snakemake config file The input and output directives are followed by lists of files that are expected to be used or created by the rule. You can set multiple --config values on the command line and the list ends when there is Each line of the yaml file begins with a label followed by a colon. Reload to refresh your session. Still doesn't understand exactly where was the mistake, if someone can explain, I'm still listening! Also note that if the output is determined based on and expand over a wildcard, this wildcards will not be available inside the rule. You still cannot get the output file name without copying it manually, but you can use a function to make it easier to name log files by using rule names as variables. First create Refers to the wrapper "0. 3. Standard Configuration. The resulting sample. yml in their root directory, which configures the usage instructions displayed Hi @543090lee and @mattdoug604, the files you posted are not MAVIS config files. Section 4 - Snakemake Patterns and Recipes; 6. If yes, is there any viable alternative strategy for this scenario? Cluster Configuration¶ Snakemake supports a separate configuration file for execution on a cluster. A configuration is provided as a JSON or YAML file and can be loaded with: The config file can be used to define a dictionary of configuration parameters and their values. Snakemake is highly popular, with on average more than 7 new citations per week in 2021, and almost 400k downloads. For pipeline's that I developed (bam2bakR, PROseq_etal, THE_Aligner, etc. Is it possible to enable/disable certain I am building a snakemake workflow that will be used with different configurations. config/config. snakefmt is able to read project-specific default values for its command line options from a pyproject. #!python #!/usr/bin/env python3 import os import sys from snakemake. e. input[0] to access the first input file snakemake --configfile config/config. I can use {input. Snakemake allows you to use configuration files for making your workflows more flexible and also for abstracting away direct dependencies to a fixed HPC cluster scheduler. Overwrite nested config options on command line. My issue is that I want to be able to add to the existing config file. --cluster-config - This specifies the location of a configuration file to read cluster Step 3: Input functions¶. In particular, it can happen that There are a number of parameters I always want to run for snakemake, and writing them on the command line every time can be tedious. tsv has a lot of columns. id, "fq1"]) are of type pandas. The application of a rule to generate a set of output files is called job. input[0] to access the first input file You still cannot get the output file name without copying it manually, but you can use a function to make it easier to name log files by using rule names as variables. ), see the configuration section for a detailed description of all parameters present in each Snakemake supports a separate configuration file for execution on a cluster. output[0], etc, I am reluctant to do so since I'd also like to be able to use them outside of snakemake. One natural way to solve this problem -- what I have been doing -- is to run def get_argument_parser (profile = None): """Generate and return argument parser. Hot Network Questions How to balance minisplits and oil furnace for winter heat? Snakemake can't find config file in path with spaces #2286. note that as Snakemake PR 1111 isn't merged yet, INI-style is only supported in vpipe. I nearly always use dedicated conda environments for each rule, so I’d like --use-conda to be How to use a list in Snakemake tabular config. I would like to do this using the following rule setup: Add that sample to the config file and see how Snakemake wants to recompute the part of the workflow belonging to the new sample, when invoking with snakemake-n--forcerun bcftools_call. In this configuration file above, I only have information for a __default__, which will be used as the default for each rule. There are a number of parameters I always want to run for snakemake, and writing them on the command line every time can be tedious. 1 - GCF_008423265. 2. yaml: the configuration files making the Snakefile adaptable to any input files, genome and parameter for the rules. I have a rule that designates certain files as temp(). That is how Snakemake works: when the Snakemake tries to constract the DAG of jobs and finds that it needs a certain file, it looks at the output section for each rule and checks if this rule can produce the required file. config[key]: Use this when the key is required, or a default is specified in a pre-loaded configuration file. Only if that fails, it will interpret the value as string. yaml"允许你从一个 YAML 文件中读取配置参数，这样可以使工作流的管理更加灵活和高效。以下是如何使用这个特性，并通过一个例子来详细说明其用法。假设你正在进行一项需要数据分析的生物信息学研究。你有多个样本需要处理，并且希望通过 Snakemake 来自动化这个 YAML is a very popular format for config files as it is very simple and human-readable. snakemake/conda) and not mess with the - I am writing a snakemake rule that uses multiple commands as shown below: rule RULE1: input: 'path/to/input. The I currently have a snakemake workflow that requires the use of lambda wildcards, set up as follows: Snakefile: configfile: "config. Using configuration files; 6. News about Snakemake are published via Twitter. bam files (one for each sample). To activate this, you have to add the top-level key __use_yte__ = true to the YAML file. As fallback, it is also possible to provide a version agnostic config. File locations Sample names and associated information Rule computing resources Etc But it is preferable to use paths to other smaller config files Same as Snakefile and snakefiles Example: Table containing the sample names and information: config/samples_info. Attention: This function needs Python docutils to be installed for the python installation you use with Snakemake. Snakemake can make use of cluster engines that support shell scripts and have access to a common filesystem, (e. yaml with X denoting the minimum supported Snakemake major version (e. Ideally I would be able to pass a parameter on commandline to determine which conf file to As the code is written above, running snakemake will fail because config["{sample}"] will literally look for the {sample} variable in the config file which doesn't exist In real life, you would want to use an external sample sheet or a config file for things like this. You should always take a look at the config file since you should not escape from the complexity of anything that will impact your findings. 0 You signed in with another tab or window. For each input file Here is an attempt at answering the question raised in your last edit (23/07/2020). I would like to do this using the following rule setup: The config file can be used to define a dictionary of configuration parameters and their values. Additionally we need the shell command 'echo "Hello How to read the config. In snakemake I would like to access keys from the config from within the shell: directive. A configuration is provided as a JSON or YAML file and can be loaded with: After some more research, it seems there is a difference between 1) parameters that are not contained in the config and 2) parameters that are contained but not set (i. A configuration is provided as a JSON or YAML file and can be loaded with: Configuration. snakemake folder and the lock folder within. This is my first snakemake workflow, so it might be that I'm overcomplicating things. A cluster config file allows you to specify cluster submission parameters outside the Snakemake Tutorial. A cluster config file allows you to specify cluster submission parameters outside the Since the first way did not work, I thought I could just make a config file with the file paths to the two config files containing the parameters: highQC: "configs/config_highQC. Is using the (deprecated) --cluster-config still the best option? If not, how should we pass non-integer, per-rule cluster options? Partitions and log files are my specific interests at the moment. Snakemake wildcard in output only. In this section, I am going to detail the process of profile creation. 2. quux} is not supported. yml to show up in the list of untracked files, I suggest you add a dummy rule with that sole purpose of tracking "untracked files", e. The first line in our example defines the name of a rule, in this case hello_world. sh, It can be tweaked and run to generate a valid config file. 1 Cluster Configuration¶ Snakemake supports a separate configuration file for execution on a cluster. MAVIS configuration files are used to specify the specific parameters you want to use for each step of the MAVIS pipeline. We import it using the configfile: notation, and so it’s easy for us to find, we place it at the very top of our Snakefile. This file needs to be a json. To learn Snakemake, please do the Snakemake Tutorial, and see the FAQ. fq1 and input. Tutorial: General use. The indentation here is important. Using IF statement for PARTIAL match of input filename in snakemake to run different shell commands. Now, we Here's the full Snakefile as a reference: input: "plots/quals. """ import configargparse from configargparse import YAMLConfigFileParser dirs = get Snakemake supports a separate configuration file for execution on a cluster. 在 Snakemake 中，configfile: "config. V-pipe can also import old INI-style configratuion by Python config parse. --configfile and --config options now work. fastq-dump SRR390728 What is a config file? Config files in Snakemake workflows are used to store and manage configuration parameters separately from the workflow script. yaml for Snakefile. Access config values appropriately . The file has to be named config. A configuration is provided as a JSON or YAML file and can be loaded with: I want to download the fastq files from SRA database using SRR ID using Snakemake. tsv In the config file: samples: 'config/samples_info. Thanks! Sounds reasonable so far. I read a file to get SRR ID using python code. 1). But there is one more thing. To properly understand what Snakemake can do for you please read our “rolling” paper. yaml as. It can be improved by making use of certain wildcards or by providing a hard copy of the output filename. My code is below. loc[wildcards. Give an example of "use PE and SE together" - I presume you don't just mean snakemake mapped/tardigrade. Finally, I succed with the pipeline removing the fq1_ID and fq2_ID variables in the rule bwa_mem_to_bam and replacing in the message of the rule input. input[0], snakemake. To activate this, you have to add the top-level key __use_yte__ = true to the YAML file. Dependencies between the rules are determined automatically, creating a DAG (directed acyclic graph) of jobs that can be I have Snakemake hooked up to an S3 account, and I'm wanting to delete certain temp() files after processing our pipeline. Per default, Snakemake will lock a working directory by output and input files. Format Config files should be YAML In this section we will learn about the params: field for rules how to pass options to Snakemake using a config file. Series. I am constructing a snakemake pipeline. Maybe it indeed got lost in the example: The names of the samples are quite long. Logs Minimal example snakemake -j 1000 -s workflow/Snakefile --use-conda --cluster-c The full post is a good reference of how Snakemake config handling works (the documentation is a bit lacking at times). Use the appropriate method to access configuration in the config global variable. A cluster config file allows you to specify cluster submission parameters outside the Snakefile. fq2. 8/bio/samtools/sort" to create the output from the input. Two instances Snakemake version V8. Accessing the path of the `--configfile` within Snakefile. config. the wildcards are replaced by the regular expression . Snakemake version version 8. Snakemake supports a separate configuration file for execution on a cluster. The output tree: 2. One new feature is that execution of jobs on a cluster or the cloud is handled by executor plugins. 1 - GCF_000021665. If you want to set specific time limits for each rule (or some rules), you can add that info to the file. I have to ensure that these commands use the correct input file paths of course (and, in this case, also the output in a coherent manner with what the output section says). Each output file will then be named something like {sample}_{target}. samples: chr1A: - scaffold26096 - scaffold40476 chr1B: - scaffold11969 - scaffold83281 - scaffold43483 chr1D: - scaffold4701 - Correctly consuming a multiline config file in snakemake as an input. txt, i. Also, keep in mind that: Using snakemake, I'm interested in splitting a bam file by it's overlap with a set of targets. Then the read group wildcard will be available in the rules upstream the one To get a first impression, please visit https://snakemake. yaml" Finally, we need to access the values in the config file. are null). yaml). yml" # This is the default_target rule which is executed The full post is a good reference of how Snakemake config handling works (the documentation is a bit lacking at times). Snakemake directly supports the configuration of your workflow. github. A yaml file which follows the syntax expected by intake, a field called sources that contains a list of nested entries that specify at the very least a (possibly local) url at which the file can I think your yaml file does not contain the data you think it does. yaml file into the Snakefile. I want to use directories or all files in directories as input in snakemake. bam. A configuration is provided as a JSON or YAML file and can be loaded with: Right now, I can manually require the cluster config file ('cluster. Then the read group wildcard will be available in the rules upstream the one Initialization features ensure that the pipeline configuration files and documentation is stored with the pipeline. This will increase progressively in complexity and we will need to add rules to the snakeFile. txt", zip, path=PATH How to read the config. Using snakemake, I'm interested in splitting a bam file by it's overlap with a set of targets. I have this other rule, bwa_mem_bam that creates a file named {sample. Also, keep in mind that: Each wildcard in the input section shall have a corresponding wildcard (with the same name) in the output section. Snakemake For this purpose, Snakemake provides a config file mechanism. – Each wildcard in the input section shall have a corresponding wildcard (with the same name) in the output section. fastq", this will run ln -s for each combination of {dir} and {sample} that is necessary to produce the output required by the downstream rules. It has to be in a subdirectory, e. I would like to run this pipeline on Snakemake already has reasonable defaults built in, which are automatically activated when using the --default-resources flag (see above, and also snakemake--help). Since we have stored the path to the FASTQ files in the config file, we can also generalize the rule bwa_map to use these paths. For simplicity, all paths should be absolute. If your configuration file is as you show, you should have a config Python dict that contains a Snakemake options. My workflow takes as input the 'database query' for downloading some files, which is specified in my 'config. If you set workdir manually within your workflow, the config file has to be in there. For example, suppose that we want to run the same Snakemake allows you to use configuration files for making your workflows more flexible and also for abstracting away direct dependencies to a fixed HPC cluster scheduler. Don't forget that all python code outside the rules is executed first so you can debug any bad configuration before any rule is executed. Individual --config items on the command line always take precedence over settings in the config file. Standard I'm using the following rules at the start of my pipeline to run fastqc and for alignment of the fastqc files: import os # read config info into this namespace configfile: Snakemake allows you to use configuration files for making your workflows more flexible and also for abstracting away direct dependencies to a fixed HPC cluster scheduler. Improve this question. 1. partition} -n {threads} --mem={params. Declare variable-length array as a config value with Snakemake CLI. Snakemake trouble accessing nested values in config. The shell directive is followed by a Python string containing the shell command to execute. The Snakemake config file holds all tunable parameters of the pipeline. summary. 0 Describe the bug The snakemake installed by Conda cannot submit tasks to the cluster for running using the --cluster parameter. A config file can also Adapting Snakemake to a particular environment can entail many flags and options. To use the Snakemake SLURM stuff, you’ll need a config file, in YAML format, often called a “profile”. yaml to define the values for the different sbatch options. I haven't tried running an example, but it seems to me that in symlink rule you want:. 0 The executor does not detect the workspace correctly and outputs all the files into the nested path. smk --cores 40 --use-conda It then fails with this message: I just used a subsetted config file to check the output of the command you suggested. Standard First we must import the config. The parameters of these runs however overlap, so I would like to create one default. NOTE: these settings are only valid for this In this configuration, Snakemake runs on the cluster login node and submits jobs. it gave me a lot headache there. The latter expects the values of types str or list[str] in the input section of the rule, but the values you provide (samples. $ snakemake--config version = 2018_1 Snakemake will first try to interpret the given value as number. For example, I nearly always want snakemake to Snakemake. We can Use a YAML config file to separate your configuration from your workflow logic; Decide if different config items should be mandatory or else have a default; Reference the To run Snakemake with a config file, pass it after the flag --config in your Snakemake command, as such: snakemake --cores 1 --config config. 8 yes it works without the add rule. The cluster config is a JSON- or YAML-formatted file that contains objects that match names of rules in the Snakefile. yaml and must be located in the working directory for the pipeline. Above, genome is a string variable with the value genome. There is a similar answer, but a more specific example for this question is as follow. utils import read_job_properties snakemake --config builds="mybuilds" In your case, my guess is that the user of the snakemake pipeline is supposed to provide a configuration file on the command line. Below is an example Inside the script, you have access to an object snakemake that provides access to the same objects that are available in the run and shell directives (input, output, params, wildcards, log, threads, resources, config), e. foo}, {output. For A quick-start guide for Snakemake. Snakemake loads the --configfile supplied on the command line, or else defaults to the one named in the Snakefile, or else runs with no config file. core. Say I have this block in the config file: wildcard_constraints: sample: '[^_/]+' reference: '[^/]+' Then in my snakefile I have: Since snakemake locks the working directory, I wonder if running the same pipeline with different config files in the same working directory would result in some conflict. I guess you want each chromosome to contain a list of scaffolds, like:. Subsampling FASTQ files; 6. Applying one rule to to many files - replacing for loops in shell scripts; 6. config file. If you want to apply samtools view once for each read group, then the expand does not belong to the output of the split_cram_by_rg rule, but to a rule downstream. sam. +. yml containing:. csv We can load this yaml using configfile. Ideally, though, I would like to be able to access the per-rule cluster config information that is passed through the --cluster-config arg. You can have as many sub-levels as you want, indicated by tabs. yaml file in which I want to store wildcard constraints. configfile: "config. The cluster config can snakemake choose a config file based on a parameter? 1. If the rule’s output matches a requested file, the substrings matched by the wildcards are propagated to the input files and to the variable wildcards, that is here also used Configuration. Use a YAML config file to separate your configuration from your workflow logic; Decide if different config items should be mandatory or else have a default; Reference the A Snakemake workflow defines a data analysis in terms of rules that are specified in the Snakefile. Snakemake directly supports the configuration of your workflow. (config["sample_file"]) BAMFILE = SAMPLES["Sample"] PATH = SAMPLES["Path"] rule all: input: expand("{path}{sample}. 0 Describe the bug When I run my previously functional snakemake file, I get a ValueError: ValueError: Invalid config definition: Config entry I'm using snakemake for the first time in order to build a basic pipeline using cutadapt, bwa and GATK (trimming ; mapping ; calling). Snakemake multiple Config Files? 3. For example, two directories with different no. toml file. This table is a bunch of rows that I first take out of a very large sample overview. A configuration is provided as a JSON or YAML file and can be loaded with: Here is an attempt at answering the question raised in your last edit (23/07/2020). g. All keywords not listed below are interpreted as paths to files that shall Is there a way to define a snakemake config string in a . A config file can also be a good place to put accessions. This case is different to the rule bcftools_call we modified above. yaml with X Snakemake allows you to use configuration files for making your workflows more flexible and also for abstracting away direct dependencies to a fixed HPC cluster scheduler. Workflows are described via a human readable, Python based This is all getting quite complex, so in summary: Snakemake loads the --configfile supplied on the command line, or else defaults to the one named in the Snakefile, or else runs I have a snakemake pipeline and different config files for different runs. This project provides Snakemake configuration profiles for various execution environments. 17. This is the way how Snakemake yaml might be a better choice for formatting the config since it's more readable. Snakemake will automatically download the wrapper from the Snakemake Wrapper Repository. Now, make sure to use **config["inputs"] as this will expand the contents of the dictionary and pass it as key=value combinations: The information within the {} are the parameters that snakemake will read from the cluster_config. Finally, sed commands can be used to replace variables with either command_line inputs or I'm using Snakemake with a tabular configuration. Create a folder called profiles #Genomics #Python #PipeliningA quick introduction on adding configuration file to your snakemake pipelineThis video is intended for those who are already fam Snakedeploy will create two folders workflow and config. I am using some python scripts with snakemake to automate the workflow. tsv: a file containing sample names and the paths to the forward and eventually reverse reads (if paired-end). Each cluster job executes a single rule and then exits. At the next stage of analysis I have to merge sequencing units (mapped . io. yml file. Follow Multiple "params" in Snakemake file. quux} is not Snakemake version version 8. yaml. Also note that if the output is determined based on and expand over a wildcard, this wildcards will not be available inside the rule. rule symlink: input: config['data'] + "{dir}/{sample}. Is there a way to define a snakemake config string in a . yaml file so that it can contain {wildcard} and {param} values, and when that string is used in a shell command, the {<name>} values are substituted with the actual value of "<name>"? data_dir is a parameter read from a config file. tsv' Finally, I succed with the pipeline removing the fq1_ID and fq2_ID variables in the rule bwa_mem_to_bam and replacing in the message of the rule input. bam M1-2. file' output: 'path/to/output. In this post, we will see how to adapt the amount of RAM, time, and the number of threads to a particular job through the profile config. Two instances creating disjoint sets of output files are possible. yaml file to output as a prefix. This file has to be adapted to your sample names before running the pipeline. Snakemake also supports the use of configuration files, where the snakefile supplies the name of the a default config file, which can be overridden on the command line. snakemake-workflow-catalog. A configuration is provided as a JSON or YAML file and can be loaded with: The given path is interpreted relative to the Configuration files are a snakemake feature that can be used to separate the rules in the workflow from the configuration of the workflow. 5. A configuration is provided as a JSON or YAML file and can be loaded with: In the previous posts, we saw how to get started with snakemake, reduce command-line options, and submit your jobs to a cluster. bam}. Share. json. bed files) and take merged . Snakemake follows the GNU Make paradigm: workflows are defined in terms of If you use a Vagrant Linux VM from Windows as described above, create that directory under /vagrant/, so that the contents are shared with your host system (you can then edit all files How to read the config. $ snakemake --config 'version="2018_1"' Per default, Snakemake will lock a working directory by output and input files. samples: chr1A: - scaffold26096 - Snakemake supports a separate configuration file for execution on a cluster. The issue seems to be that although both runs are using data in different folders snakemake creates the lock on the pipeline folder due to the . By this, the rule can produce all files that follow the regular expression pattern . A configuration is provided as a JSON or YAML file and can be loaded with: Loading from the config file. smk files have access to the To generate the target files, Snakemake applies the rules given in the Snakefile in a top-down way. Has the two files contain the same information in different formats, I'd like to remove the first one Hi, I was trying to run my pipeline but I am encountering this error: MissingRuleException: No rule to produce --cluster=sbatch --partition={resources. but I have programs that generated a random name and I want to pass that random name from config. I want to parse the Variable one by one as input. frame. toml and use any configuration there. Setting up a SLURM profile config. usage: mandatory-flags: # optional definition of additional flags desc: # describe your flags here in a few sentences (they will be Right now, I can manually require the cluster config file ('cluster. Still doesn't understand exactly where was the mistake, if someone can explain, I'm still listening! Cluster configuration for snakemake. Inside the script, you have access to an object snakemake that provides access to the same objects that are available in the run and shell directives (input, output, params, wildcards, log, threads, resources, config), e. yaml file that I think your yaml file does not contain the data you think it does. 0 The first line in our example defines the name of a rule, in this case hello_world. There are few (if any) scientific questions that you can answer by running a single program or script. Configuration. You need to convert them to what Snamemake expects. Please consider contributing your own if it is still missing. In this Section: In our previous workflow, two of our steps, The profile folder is expected to contain a configuration file that file that defines default values for the Snakemake command line arguments. Snakemake version 8 introduces breaking changes with respect to the Snakemake cookiecutter profile. 2,881 1 1 Configuration. fa and samples is a list with the variables ['A','B','C']. yaml'. you can use snakemake. Cluster Configuration¶ Snakemake supports a separate configuration file for execution on a cluster. err can snakemake choose a config file based on a parameter? 1. In addition, it will also load any black configurations you have in the same file. maybe it's because of i'm used to the way Cluster Configuration¶ Snakemake supports a separate configuration file for execution on a cluster. – I am new to snakemake. and here's the result: 4880 get_fastq_for_subset. A good example would show some example input files, a snakemake invocation, and the expected output. MSR MSR. simple/ Open it in your favorite text editor and replace all the placeholders surrounded in angle brackets (<>) with the options you use to submit jobs on your cluster snakemake --config builds="mybuilds" In your case, my guess is that the user of the snakemake pipeline is supposed to provide a configuration file on the command line. Therefore, since Snakemake 4. yaml" workdir: config["work"] rule all: input: expa Since the deprecation of cluster configuration files the ability to specify per-rule cluster settings is snakemake-profile-specific. havardtl opened this issue Jun 6, 2023 · 0 comments Labels. I ended the previous post by mentioning resources that were set by default. v8+. yaml One option is to use an external module, intake, to handle the environmental variable integration. By default, snakefmt will search in the parent directories of the formatted file(s) for a file called pyproject. In your case, it is possible that you Snakemake supports a separate configuration file for execution on a cluster. I want to run command. This file will specify all the necessities of the cluster configuration so that Snakemake can submit jobs on your behalf as governed by the workflow. Hot Network Questions Cluster Configuration¶ Snakemake supports a separate configuration file for execution on a cluster. yml ## # longitudinal analysis perform_longitudinal: 'yes' # yes for longitudinal analysis When 'yes' is entered in the configuration Snakemake will include additional variables in rule all and run an addition Snakefile to generate these files. the Sun Grid Engine). +/file\. A wrapper script with an example invocation can be found in run_make_config. 0. 4. 6. yaml file and feed it in snakemake. Correctly consuming a multiline config file in snakemake as an input. fa", get_bwa_map_input_fastqs. csv demo: data/demo. MAVIS configuration files are used to specify the specific parameters you want to use for Snakemake can't find config file in path with spaces #2286. sample] input: "data/genome. Or are you trying to share files? - that's simply a matter of adjusting the output of get_fastq_reads. {wildcards}. config; snakemake; Share. Sometimes, shell commands are not only composed of input and output files and some static flags. Motivation. Using multiple filenames as wildcards in Snakemake. Snakemake. Now we need to tell Snakemake where to find the configuration file. A Snakemake rule has a name (here bwa_map) and a number of directives, here input, output and shell. Thereby, 0. In the config/ directory you will find a file named config. A configuration is provided as a JSON or YAML file and can be loaded with: I am running a snakemake pipeline from the same working directory but with different config files and the input / output are in different directories too. svg" return config["samples"][wildcards. Never fail me - how to make shell commands always succeed; 6. --cluster-config - This specifies the location of a configuration file to read cluster The information within the {} are the parameters that snakemake will read from the cluster_config. err (without an intermediate directory) can lead to a very overwhelming 'logs' directory. Follow asked Apr 15, 2021 at 12:41. Preparing a config file from scratch for a given workflow could be quite a strenuous task. DataFrame or pandas. Here, we define two wildcards, dataset and group. In concrete terms, I have a rule bwa_mem_sam that creates a file named {sample}. The part following shell: tells Snakemake that this rule executes a shell command, which in our case prints Hello World! to the console. of bam files, --M1 M1-1. Improve this answer. I used a configuration file to pass the statements to the Snakefile ## Config. Best practices for writing Snakemake workflows can be found here Snakemake supports a separate configuration file for execution on a cluster. bam --M2 A quick-start guide for Snakemake. If your configuration file is located somewhere The problem is that you setup your global wildcard constraints wrong: wildcard_constraints: separator = config["separator"], extension = config["file_extension def report (text, path, stylesheet = None, defaultenc = "utf8", template = None, metadata = None, ** files): """Create an HTML report using python docutils. series. Most commonly, rules consist of a name, input files, output files, and a shell Configuration. Step 4: Rule parameters. For aggregation over many files, Snakemake provides the So far, we have always specified a It downloads some read files from a website, decompresses them, That isn’t the only way to solve that problem, we could also hardcode this or write it in a config file that is Configuration. You signed out in another tab or window. To understand this, it is important to know that Snakemake workflows are executed in three phases. . In the simplest case, these are just explicit Python strings. The problem is that you setup your global wildcard constraints wrong: wildcard_constraints: separator = config["separator"], extension = config["file_extension What you need seems to be a checkpoint rule which is first executed and only then snakemake determines which . You also generate a list of sample identifiers, and store it in the list SAMPLES. +\. 2 Snakemake specifying configuration parameter from nested config. The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. fq1_ID and input. baz}, but {config. These scripts take in command line arguments and, while I could replace them with snakemake. yaml --batch get_fastq_for_subset=1/20 --snakefile Snakefile-compute. I have a config. For instance, there is a dedicated executor plugin for SLURM that provides much of the functionality that was previously catered for by this snakemake profile. memory}GB -o {log}. The profile folder is expected to contain a configuration file that file that defines default values for the Snakemake command line arguments. Snakemake detects the creation of output files, and submits new jobs (rules) once their dependencies are created. The config file is a mandatory input of all workflows, even if you are fine with all default parameters. 1 - GCF_000020225. How to use include directives with specific config files in snakemake? How to read the config. Config files can be written in JSON or YAML, and loaded with the configfile directive. This is the number I expect. yaml file. If the rule’s output matches a requested file, the substrings matched by the wildcards are propagated to the input files and to the variable wildcards, that is here also used We now support modern JSON / YAML config format as supported by Snakemake. {SE,PE}. yaml file so that it can contain {wildcard} and {param} values, and when that string is used in a shell command, the {<name>} values are substituted with the actual value of "<name>"? Inside the script, you have access to an object snakemake that provides access to the same objects that are available in the run and shell directives (input, output, params, wildcards, log, threads, resources, config), e. If your configuration file is as you show, you should have a config Python dict that contains a "contigs" entry, which is in turn a dict that can associate lists of numbers to sample identifiers. I have a Snakemake workflow where one of the top-level config entries is an array of variable size (in this particular example, a sibling may or may not be included in the analysis). yaml file on the command line. 1, it is possible to specify a configuration profile to be used to obtain Snakemake will load the config file and store its contents into a globally available dictionary named config. Here's an example adapted: I'm struggling to fully understand the file and folder structure you get after cloning your git repo. In this case, Snakemake simply needs to be given a submit command that accepts a shell script as first positional argument: # access property defined in the cluster configuration file (Snakemake >=3. Typically written in YAML format, these files contain key-value pairs representing various parameters such as file paths, resource requirements, and other settings that control the behavior of the How to read the config. 0 Describe the bug When I run my previously functional snakemake file, I get a ValueError: ValueError: Invalid config definition: Config entry must start with a valid identifier. snakemake rules: Passing on variables outside of the file name. inputs: labs: data/labs. In our case, it makes sense to specify the samples in config. yaml Thanks for the point! I can get this to work if I know the exact input file name and they stay the same through the whole pipeline and just let snakemake infer from them. bar}, and {params. Hot Network Questions QGIS : Want to create "polygons with hole" instead of "overlaping polygons" when use of "contour tool" A fantasy movie with two races, "Big Ones" (=us) and smaller ones, about saving a newborn baby from a cruel queen If you want don't want config. json files are present and runs your extract/aggregate functions. Is there a way to Snakemake specifying configuration parameter from nested config. We need the shell command to be indented in one TAB space from rule. Open havardtl opened this issue Jun 6, 2023 · 0 comments Open Snakemake can't find config file in path with spaces #2286. In our example workflow, we add the Snakemake also supports the use of configuration files, where the snakefile supplies the name of the a default config file, which can be overridden on the command line. Per-rule configuration must be placed in a file called lsf. This is the way how Snakemake Inside the script, you have access to an object snakemake that provides access to the same objects that are available in the run and shell directives (input, output, params, wildcards, log, threads, resources, config), e. The message is less elegant, but the pipeline is running correctly. Configuration values are available as a config dictionary provided in scope afterwards. All rules of the include: *. out -e {log}. fq2_ID by input. yaml to your Snakemake project. yml in their root directory, which configures the usage instructions displayed by this workflow catalog. The config file can be used to define a dictionary of configuration parameters and their values. Add this line to the top of your Snakefile. """ import configargparse from configargparse import YAMLConfigFileParser dirs = get Download the configuration file config. Not with --configfile option. utils import read_job_properties would print a list containing all config files, but running snakemake --configfile [path/to/config/file] -j 1 simply prints an empty list (Snakemake 6. Workflows are described via a human readable, Python based language. This includes creating output dirs, not included in snakemake and copiying configuration files that are utilized within the pipeline. I use Snakemake Tabular (mapping with BWA mem) configuration to describe my sequencing units (libraries sequenced on separate lines). This is deprecated in favor of the --report flag. You are trying to pass the objects from pandas to Snakemake. input[0] to access the first input file Add that sample to the config file and see how Snakemake wants to recompute the part of the workflow belonging to the new sample, when invoking with snakemake-n--forcerun bcftools_call. config. For example, I nearly always want snakemake to “keep going” (--keep-going) with independent jobs, even if a single one fails. In the workflow, the configuration is accessible via the global variable config, e. Or instead of doing this, be able to run a python script that sets global In snakemake I would like to access keys from the config from within the shell: directive. Two instances def get_argument_parser (profile = None): """Generate and return argument parser. Subsetting FASTQ files to a fixed number of records; 7. Options under the __default__ header apply to all rules, but it's possible to override them selectively with rule-specific options. contain a YAML file . One natural way to solve this problem -- what I have been doing -- is to run Hi @543090lee and @mattdoug604, the files you posted are not MAVIS config files. In particular, it can happen that With many samples, the flat structure of logs/{rule}. yaml" Snakemake does not support different configfiles for different rules or rule files if they are within the same main Snakefile. If you open it in a text editor, you will see several parameters which you can alter to your heart's content. The set of targets are defined by a bed file per sample. input[0] to access the first input file In a more useful context with direct integration in the workflow: I iterate over the list of pools (config['pools']) in the config file and with via the index information, simultaneously draw the corresponding sample to barcodes (config['name2bc'][idx]) dictionary, in which the known name to barcodes mappings are stored, similar to c2n in my original example (In my actual You can use the Conda configuration option pkgs_dirs to set package cache locations. This tutorial introduces the text-based workflow system Snakemake. An example of a config can be found at mini-tutorial. Check this section for a complete list and relative explanation. yml" # Include all files you want considered "tracked" by snakemake rule track_files: input: "config. 3 ways are supported, but only 2 should be used:. For this we create a configuration file named cluster. It means that I do not know the names of the files that will be downloaded before running the pipeline. In case of YAML, the file can optionally be processed with YTE. Using split to split up files; 6. 0. json') as a hardcoded input. Let's pretend we have config. MPI jobs¶ Snakedeploy will create two folders workflow and config. vX+. Snakemake follows the GNU Make paradigm: workflows are defined in terms of rules that define how to create output files from input files. Two Snakemake instances that want to create the same output file are not possible. Snakemake specifying configuration parameter from nested config. Consider: accessions: - GCF_000017325. 1. file' shell: 'path/to/command1 {input} | /path/to/ Variables as path2 above are often stored in a config-file accessed by the snakemake directive configfile: If all your files are on the same path, In this configuration, Snakemake runs on the cluster login node and submits jobs. 1 snakemake module from github changes targets? 0 Relative paths in config. I don't see how to use a Snakemake rule to remove a Snakemake output file that has become useless. If the pipeline itself is already on the same file system as the Conda package cache, I would just let Snakemake use the default location (. slurm. : configfile: "config. I am very new to snakemake and also not so fluent in python (so apologies this might be a very basic stupid question): I am currently building a pipeline to analyze a set of bamfiles with atlas. Currently I'm using the following config file. To use this config file in our pipeline, we can pass it when we run it like so: Snakemake -j 1 --configfile config. You switched accounts on another tab or window. I'll test it right away. lib2data is a function that generates commands based on the values of some wildcards. Snakemake perform rules based on configs. config/samples. ttqxrb jifd clcji zjiuq adfkkp fkjg omlpc nnqhkl tytxld arri