czbiohub-sf nf-predictorthologs issues

czbiohub-sf / nf-predictorthologs

*de novo* orthologous gene predictions from bam + bed or fasta/fastq data

MIT License

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issues

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Hot Install Docker Container

#92 Montana opened 3 years ago
2
Update bed + bam input params

#91 olgabot closed 3 years ago
0
Protein fasta input fixes

#90 olgabot closed 3 years ago
0
Add option to skip diamond and sourmash search

#89 olgabot closed 3 years ago
0
sencha version in get_software_versions and increase version for sencha

#88 pranathivemuri closed 3 years ago
1
Differential hash expression -- proof of concept updates

#87 olgabot closed 3 years ago
0
Update Docker, dependencies for sencha

#86 pranathivemuri closed 3 years ago
1
human host removal

#85 lekhakaranam closed 3 years ago
1
added minimap to dependencies

#84 lekhakaranam closed 3 years ago
1
Fix skip trimming and QC

#83 olgabot closed 3 years ago
2
Propagate molecule and k-mer size to sample id in sencha translate

#82 olgabot closed 4 years ago
1
Get hashes from each sample

#81 olgabot opened 4 years ago
0
Update sourmash

#80 olgabot closed 4 years ago
1
For diff hash, do sourmash search then diamond on unassigned hashes

#79 olgabot closed 3 years ago
7
sencha translate processes try - placeholder when translate works with cpus - this will correct changelog and merge

#78 pranathivemuri closed 3 years ago
1
Updates for differential hash expression

#77 olgabot closed 4 years ago
2
Update sambamba labels for cpu, memory, time requirements

#76 olgabot closed 4 years ago
1
Don't filter reads for size after trimming

#75 olgabot closed 4 years ago
2
olgabot/infernal cmSCAN not search

#74 olgabot closed 4 years ago
3
Create environment_hulk.yml

#73 pranathivemuri closed 4 years ago
0
Multiplex "sencha translate" parameters

#72 olgabot closed 4 years ago
1
no more warnings

#71 phoenixAja closed 4 years ago
0
ksize, molecule passing from csv into all processes

#70 pranathivemuri closed 4 years ago
2
tokenized ksizes for sencha translate and sencha index

#69 phoenixAja closed 4 years ago
10
fixing samtools fastq

#68 phoenixAja closed 4 years ago
1
make_protein_index only happens for one ksize,molecule pair but should happen for the cartesian product

#67 olgabot closed 4 years ago
3
fastp --trim_poly_x for paired end reads, too!

#66 olgabot closed 4 years ago
0
Rename: bam_name_full --> bam_dedup

#65 olgabot closed 4 years ago
2
Phoenix/sambamba

#64 phoenixAja closed 4 years ago
3
Use "sourmash gather" instead of searching individual hashes

#63 olgabot opened 4 years ago
1
modify csv

#62 pranathivemuri closed 4 years ago
4
Add parser for INFERNAL output

#61 olgabot opened 4 years ago
0
Actually do --low_complexity_filter for fastp

#60 olgabot closed 4 years ago
2
Add hmmer search of Dfam for noncoding RNAs

#59 olgabot opened 4 years ago
0
Update DIAMOND version

#58 olgabot closed 4 years ago
0
Use sambamba to remove duplicates of bam files

#57 olgabot closed 4 years ago
12
Add workflow overview image

#56 olgabot closed 4 years ago
2
Add Infernal for RNA search to dependencies

#55 olgabot closed 4 years ago
0
Add INFERNAL for noncoding RNAs, diamond makedb optimizations

#54 olgabot closed 4 years ago
2
For nucleotide input + diamond search, add option to do `diamond blastx`

#53 olgabot opened 4 years ago
0
Add nice MultiQC summary assigning hashes to genes

#52 olgabot opened 4 years ago
1
Add csvtk to dependencies changelog

#51 olgabot closed 4 years ago
0
Index fasta files by containing hashes, and bam files by containing read ids

#50 olgabot opened 4 years ago
2
Specify multiple ksizes, molecule types, and scale sizes in the csv

#49 olgabot opened 4 years ago
0
add low complexity filtering to fastp step

#48 bluegenes opened 4 years ago
0
Do diamond search as a backup when hashes don't match in sourmash

#47 olgabot opened 4 years ago
0
Bump sourmash version to 3.3.0

#46 olgabot closed 4 years ago
0
add nf- to URL for githb actions

#45 olgabot closed 4 years ago
0
Actually support precomputed --sourmash_index ...

#44 olgabot opened 4 years ago
0
rename khtools to sencha

#43 pranathivemuri closed 4 years ago
0