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This repository has been archived by the owner on Mar 17, 2023. It is now read-only.

Issues: czbiohub-sf/nf-predictorthologs

23 Open 6 Closed
23 Open 6 Closed
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Issues list

Hot Install Docker Container
#92 opened Feb 8, 2021 by Montana
2
Get hashes from each sample
#81 opened Aug 13, 2020 by olgabot
Use "sourmash gather" instead of searching individual hashes
#63 opened Jul 17, 2020 by olgabot
1
Add parser for INFERNAL output
#61 opened Jul 16, 2020 by olgabot
Add hmmer search of Dfam for noncoding RNAs
#59 opened Jun 29, 2020 by olgabot
3 tasks
For nucleotide input + diamond search, add option to do diamond blastx
#53 opened May 19, 2020 by olgabot
Add nice MultiQC summary assigning hashes to genes
#52 opened May 18, 2020 by olgabot
1
Index fasta files by containing hashes, and bam files by containing read ids
#50 opened May 14, 2020 by olgabot
@pranathivemuri @phoenixAja
2
Specify multiple ksizes, molecule types, and scale sizes in the csv
#49 opened May 12, 2020 by olgabot
add low complexity filtering to fastp step
#48 opened May 12, 2020 by bluegenes
Do diamond search as a backup when hashes don't match in sourmash
#47 opened May 12, 2020 by olgabot
Actually support precomputed --sourmash_index ... bug Something isn't working help wanted Extra attention is needed
#44 opened Apr 30, 2020 by olgabot
Don't require signatures to be separated by aligned/unaligned
#40 opened Apr 28, 2020 by olgabot
1
Potentially use kaamer instead of diamond
#32 opened Apr 13, 2020 by olgabot
1
Add parser to summarize diamond output
#30 opened Apr 10, 2020 by olgabot
1
Add step to filter for only NP_ sequences from NCBI
#28 opened Apr 10, 2020 by olgabot
Add documentation
#23 opened Mar 6, 2020 by olgabot
Support input of DNA or protein fasta files
#21 opened Mar 4, 2020 by olgabot
Support input of multiple bam files with --bam '*{.bam,.bam.bai}'
#19 opened Mar 3, 2020 by olgabot
Test single vs paired end bam files
#18 opened Mar 3, 2020 by olgabot
Add option to skip FastQC and trimming
#15 opened Feb 26, 2020 by olgabot
Support input of multiple bed files
#10 opened Feb 25, 2020 by olgabot
Add MultiQC for khtools
#5 opened Feb 20, 2020 by olgabot
1
ProTip! Exclude everything labeled bug with -label:bug.