BAM | Binary Analysis Metadata tool gathers information | Reverse Engineering library

You may use this awk that loops through all the fields and matches a field using regular expression ^P[LR]:Z: and appends it into a variable to print it in the end.

I suggest with bash:

For doing all the replacements in a single awk call you could do:

Here is a brief example

1. Create your smoothCon object, using x

Issues like this almost always involve the use of multiple input channels:

When two or more channels are declared as process inputs, the process stops until there’s a complete input configuration ie. it receives an input value from all the channels declared as input.

Your initial assessment was correct. However, the reason only three processes were run (i.e. one sample for each of the three chromosomes), is because this line (probably) returned a list (i.e. a java LinkedList) containing a single element, and lists behave like queue channels:

We may need to serialize the inner class object and we would need to deserialize it using deserializeUntyped method for holding the inner class members variables into a map.

Troy Comi has already answered your question in comments, but I will explain it further.

Indeed, removing double braces will help. The difference between single and double braces is that double braces escape the symbol '{' and '}'. In other words whenever Snakemake encounters a string like this one "{{sample}}/{sample}_phased_illumina_FILT5.vcf.gz" in the output section, it treats {sample} as a wildcard and {{sample}} as a string "{sample}". So it tries to find the files like {sample}/saturna_phased_illumina_FILT5.vcf.gz which it definitely fails to find.

The problem is quite different in case of using this string in the expand function:

I spent a large amount of time making things self-contained. Among the many changes:

1. you should not have the base class serializing the derived (that's classic OOP), instead Boost expects derived classes to serialize their base_object<> (allowing static polymorphism and, incidentally, type registration)

2. of course, the base class should serialize its data members (type)

3. the base class SHOULD have a virtual destructor (otherwise deleting through unique_ptr's destructor will be unspecified

   Up till here:

Unfortunately, you have to deal with the namespace in the file. So try it this way: