transXpress transXpress-nextflow issues

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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issues

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Use Singularity?

#20 photocyte opened 4 years ago
1
All sequence aligned annotations should be in GFF3 format?

#19 photocyte opened 4 years ago
0
No way to specify directionality of reads

#18 conchoecia closed 5 years ago
2
samples.txt separator

#17 tomas-pluskal closed 5 years ago
1
deeploc very slow on real datasets

#16 photocyte opened 5 years ago
3
Finish implementing deeploc results in the python script

#15 photocyte closed 5 years ago
1
FASTQC checking of reads?

#14 photocyte opened 5 years ago
0
Resolve dependencies with conda?

#13 photocyte opened 5 years ago
0
test datasets should include multiple libraries/samples

#12 photocyte closed 5 years ago
1
Resuming of pipeline is non ideal

#11 photocyte closed 5 years ago
2
LSF forgetfulness?

#10 photocyte opened 5 years ago
0
Put signalp / tmmhmm after Transdecoder.Predict

#9 photocyte closed 5 years ago
0
Simple non-strand-specific test dataset + assembly renaming based on date / genus / species

#8 photocyte closed 5 years ago
0
Initial downloading of Sprot seems to hang

#7 photocyte closed 5 years ago
4
more reasonable min kmer coverage

#6 photocyte closed 5 years ago
0
BUSCO analysis of assembly

#5 photocyte opened 5 years ago
2
Calculation of heterozygosity / multiple haplotypes

#4 photocyte opened 5 years ago
0
Taxon specification at pipeline start

#3 photocyte closed 5 years ago
0
Unique naming of produced transcripts / transcriptome files

#2 photocyte closed 5 years ago
3
Transdecoder.Predict

#1 photocyte closed 5 years ago
7