FastQC | quality control analysis tool for high throughput | Genomics library

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I think it's due to you used expand function in a wrong way, expand only accepts two positional arguments, where the first one is pattern and the second one is function (optional). If you want to supply multiple patterns you should wrap these patterns in list.

After some studying on source code of snakemake, it turns out expand function doesn't check if user provides < 3 positional arguments, there is a variable combinator in if-else that would only be created when there are 1 or 2 positional arguments, the massive amount of positional arguments you provide skip this part and lead to the error when it tries to use combinator later.

Source code: https://snakemake.readthedocs.io/en/v6.5.4/_modules/snakemake/io.html

First, glob_wildcards(INPUTDIR + "{basenames}_R1.fastq.gz") returns a Wildcards object that contains the key:value pair for each wildcard. If you want to get the basenames, it should be glob_wildcards(INPUTDIR + "{basenames}_R1.fastq.gz").basenames

Second, I assume all fastq.gz files are generated by decompress_h1n1 checkpoint, since you already include the fastqc output in aggregate_decompress_h1n1 function. You shouldn't include those outputs again in rule all, it leads to snakemake try to do fastqc before checkpoint got executed.

Third, you should also put your trim_qc outputs in the aggregate_decompress_h1n1 function, basically it's the same issue as fastqc, probably the same for salmon related rules too.

There might be a potential issue, I noticed you use wrapper for fastqc, I remember that official fastqc wrapper requires the output must have html and zip, while you have a raw prefix. But I didn't see a 0.80.3 release in official document, not sure if you are using some other repository to access wrapper

By issues command snakemake -np Snakefile you are asking snakemake to produce Snakefile, and it doesn't know how to do it.

If your file is named Snakefile, there is no need to specify its name, if it has a different name then you can specify it using -s option. So right now, running snakemake -n should be sufficient to show you what snakemake would run.

I was able to figure this out, with a lot of trial and error.

Assigning a variable to a process output acts like the .out property of said process. So I set the same variable for the two exclusive processes, set the same outputs (as seen in the question) and then accessed them directly without using .out:

From your comments I gather that what you really want to do is run a flexibly configured number of QC methods and then summarise them in the end. The summary should only run, once all the QC methods you want to run have completed.

Rather than forcing the MultiQC rule to be executed in the end, manually, you can set up the MultiQC rule in such a way that it automatically gets executed in the end - by requiring the QC method's output as input.

Your goal of flexibly configuring which QC rules to run can be easily achieved by passing the names of the QC rules through a config file, or even easier as a command line argument.

Here is a minimal working example for you to extend:

Solved by providing a jobscript (--jobscript SCRIPT) with:

This is an error from python as the rule all has two functions separated by a comma. In this case the second expand call is causing the error. You could replace the , with a + to resolve the error like given below.

In your rule all you have: