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transXpress / transXpress-nextflow

transXpress: a Nextflow pipeline for rapid de novo transcriptome assembly and annotation
GNU General Public License v3.0
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No way to specify directionality of reads #18

Closed conchoecia closed 5 years ago

conchoecia commented 5 years ago

A lot of commonly-used RNA-seq library prep kits produce directional reads where the first read is antisense. Trinity and RNAspades have options to specify the directionality of the reads to help the assembly (--SS_lib_type RF in Trinity and --ss-rf in RNAspades).

photocyte commented 5 years ago

We do have support for this - wasn't fully implemented but now works for both trinity and rnaSPAdes. It's handled using nextflow profiles currently.

Using the ./run.sh wrapper script, can use the 1st parameter for the assembler, and the 2nd parameter to input the profile:

./run.sh trinity strandSpecific_local

The "profiles" block in the nextflow.config file has the currently available profiles. It's a bit verbose, and since the mode of execution (local vs cluster) is also handled via the profile, there might be a cleaner/simpler way to handle these types of parameters in the future.

photocyte commented 5 years ago

(p.s. didn't mean to close exactly, of course open to any comments on the implementation)