flowcraft

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Merging syntax with new operator

7

At the moment, Flowcraft does not provide syntax in the pipeline string to define merge of outputs from multiple components into a single component . To allow that, a new...

bfrgoncalves

unit tests for scripting templates

2

Now that we removed the dependency on the submodule and have the python templates within the repo, maybe we should start thinking in adding unit tests for some of the...

tiagofilipe12

At the moment `--merge_params` argument allow us to merge all the parameters that are repeated through the pipeline, while not providing this option will make a unique parameter for each...

tiagofilipe12

Interleaved paired-end FASTQ file [feature request]

9

I prefer using interleaved paired-end FASTQ, for example as output by `seqtk mergepe`. Does or could Flowcraft support this format?

sjackman

ERROR ~ No fastq files provided with pattern: 'pe_*.fastq.gz'

6

The command ```sh nextflow run spades.nf --fastq 'pe_*.fastq.gz' ``` produces the error ``` ERROR ~ No fastq files provided with pattern:'pe_*.fastq.gz' ``` This command ```sh nextflow run spades.nf --fastq "pe_{1,2}.fastq.gz"...

sjackman

Handle single fastq files as inputs

8

Right now, assemblerflow accepts only paired end read files (fastq), however it would be handy to add support for single fastq files.

tiagofilipe12

remove unused templates while building

1

Currently `flowcraft build` copies all python template scripts (associated to different modules) when building a new pipeline. However in some cases we don't use all those templates because the modules...

tiagofilipe12

Add optional extra params to processes

7

An option to add extra params that we currently do not contemplate in the process is necessary as it will allow users to customise the process. A possible solution is...

cimendes

Currently, Compiler processes receive data from all pipeline components that emit data to that compiler. This is usually the desired behaviour. The exception is when there is a fork in...

ODiogoSilva

Characters such as "-" should be forbidden in parameter names

ODiogoSilva