wildcards | A simple C header-only template library implementing | File Utils library

I think the problem is that rule catFasta doesn't contain the wildcard barcode. If you think about it, what job name would you expect in {wildcards.barcode}.{rule}.{jobid}?

Maybe a solution could be to add to each rule a jobname parameter that could be {barcode} for guppyplex and minion and 'all_barcodes' for catFasta. Then use --jobname "{params.jobname}.{rule}.{jobid}"

No, there isn't a way can specify two wildcards path.

According my experience, the easiest way is that you can create two copy active in one pipeline:

1. Copy active1: copy the files end with *.csv.
2. Copy active2: copy the files end with *.xml.

For your another question,there are many ways can achieve it. You could add an if condition to filter the condition: only copy active 1 and 2 both true/succeeded:

You also could do like@Nandan said:

You need to add select new { s, sd, p, r, o, u } after your last join

The rule that fails is rule guppyplex, which looks for an input in the form of {FASTQ_PATH}/{{barcode}}.

Looks like the wildcard {barcode} is filled with barcode49/barcode49.consensus.fasta, which happened because of two reasons I think:

First (and most important): The workflow does not find a better way to produce the final output. In rule catFasta, you give an input file which is never described as an output in your workflow. The rule minion has the directory as an output, but not the file, and it is not perfectly clear for the workflow where to produce this input file.

It therefore infers that the {barcode} wildcard somehow has to contain this .consensus.fasta that it has never seen before. This wildcard is then handed over to the top, where the workflow crashes since it cannot find a matching input file.

Second: This initialisation of the wildcard with sth. you don't want is only possible since you did not constrain the wildcard properly. You can for example forbid the wildcard to contain a . (see wildcard_constraints here)

However, the main problem is that catFasta does not find the desired input. I'd suggest changing the output of minion to "nanopolish/{barcode}/{barcode}.consensus.fasta", since the you already take the OUTDIR from the params, that should not hurt your rule here.

Edit: Dummy test example:

From that same documentation page - you can register a package and all interfaces in the package will be registered. This is far less verbose than registering mappers individually:

I think this is what you want...

Input file fasta.fasta is:

Using [...] to index into the .DataBases collections corresponds to the parameterized .Item[] property, which supports (a) targeting a database by numerical index or (b) by verbatim name - using patterns to match database names is not supported.

Therefore, you need to filter the database collection explicitly, which you can do with the .Where() array method, combined with member enumeration, which allows you to call the .Drop() method on every matching database:

Postgresql requires that string values are quoted with single quotes.

Python strings can be bounded with either single quotes ('...'), double-quotes ("...") or tripled single or double quotes ('''...''').

To keep Postgresql happy, use single quotes to quote the values in the query, and bound the query string with one of the other types.

Here is one way to achieve this: