flowcraft

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Flowcraft report instructions are missing in the entry README

jacarrico

Change docs instructions from using 'templates' as submodule

1

Usage descriptions of the `flowcraft/templates` folder as a submodule need to be updated/removed. As I followed the directions to find out more, I realized the repo code had been updated...

cometsong

Secondary channel for long reads

11

I'd like to add a parameter `--long-fastq` for use by `porechop` and `unicycler`. When `porechop` is used, it consumes the raw long reads, and its outputs is the input to...

sjackman

https://github.com/phac-nml/ecoli_serotyping

cimendes

https://github.com/phac-nml/mob-suite

cimendes

momps, mlst results overwrite when pipeline is resumed

1

Both these components have a a compile_results processes that combines the results and appends them into a single report.tsv file. This file is then symlinked to the publishDir folder. Upon...

cimendes

Currently, the true_coverage module requires a species to be passed on as an argument, but a scheme is not available for every species. When this happens, the pipeline breaks with...

cimendes

remove trimmomatic log

1

Due to the very high IO necessary for trimmomatic's log production, some machines will halt this process to a crawl. A fix has been done in PR #178 but I...

cimendes

Automatically set local executor CPU limit

1

Currently, the default number of CPUs used by the local executor is as follows in the `nextflow.config` file: ``` executor { $local { cpus = 4 } } ``` It...

bfrgoncalves

Merging inspect and report

3

Using flowcraft repeateadly I arrived to the conclusion that if the report can be only a flag on the inspect mode it would be better and would avoid to have...

jacarrico