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czbiohub-sf
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nf-predictorthologs
*de novo* orthologous gene predictions from bam + bed or fasta/fastq data
MIT License
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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
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