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nf-core
/
kmermaid
k-mer similarity analysis pipeline
https://nf-co.re/kmermaid
MIT License
19
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12
forks
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Update process configurations
#59
olgabot
closed
4 years ago
1
Merge in nf-core template
#58
olgabot
closed
4 years ago
6
Snafees/10x bam
#57
snafees
closed
4 years ago
2
Add docker build github action
#56
olgabot
closed
4 years ago
1
Snafees/10x bam
#55
snafees
closed
4 years ago
1
Snafees/10x bam
#54
snafees
closed
4 years ago
0
Replace conflicting things
#53
olgabot
closed
4 years ago
0
Merged template updates maybe
#52
olgabot
closed
4 years ago
0
Explicitly state tqdm version
#51
olgabot
closed
4 years ago
0
Upgrade tqdm to 4.29.1 for tqdm.auto
#50
olgabot
closed
4 years ago
1
Environment updates for aligned/unaligned 10x bams
#49
olgabot
closed
4 years ago
1
Add 10x tgz input support with extracting aligned/unaligned reads
#48
olgabot
closed
4 years ago
9
Add support for aligned/unaligned reads from 10x bam files
#47
olgabot
closed
4 years ago
0
[WIP] Add fastp support
#46
olgabot
closed
4 years ago
0
remove redundant code, change the link to test-datasets
#45
pranathivemuri
closed
4 years ago
2
remove redundant bam2fasta installation
#44
pranathivemuri
closed
4 years ago
2
Add social preview image
#43
maxulysse
closed
4 years ago
0
Revert "change docker.enabled to enabled"
#42
pranathivemuri
closed
4 years ago
0
change docker.enabled to enabled
#41
pranathivemuri
closed
4 years ago
0
added extract coding, tested on travis, added docker.tmp="auto"
#40
pranathivemuri
closed
4 years ago
7
Switch to github actions at some point
#39
olgabot
closed
4 years ago
2
Add option for input as protein
#38
olgabot
closed
4 years ago
1
Support long reads for extract_coding
#37
olgabot
closed
4 years ago
1
Do extract coding ln LSF cluster
#36
olgabot
closed
4 years ago
1
Update R package requirements to be inline with nf-core/rnaseq
#35
olgabot
closed
4 years ago
0
updated changelog.md
#34
snafees
closed
4 years ago
0
Update versions for r-base and bioconductor-edger to latest versions as in nf-core/rnaseq
#33
olgabot
opened
4 years ago
0
Output "compare" into its own directory
#32
olgabot
closed
4 years ago
1
Write sketches to folders based on the sketch ID
#31
olgabot
closed
4 years ago
1
Template merge
#30
phoenixAja
closed
4 years ago
1
Checklist for 1.0.0 release
#29
olgabot
closed
4 years ago
16
Specify 'docker.tmp = "auto"' for docker profile
#28
olgabot
closed
4 years ago
2
Only allow PRs to master from dev
#27
olgabot
closed
4 years ago
1
Actually lint the pipeline code
#26
olgabot
closed
4 years ago
1
Update to use nf-core/tools with TEMPLATE branch
#25
olgabot
closed
4 years ago
2
No space left on device for bam
#24
olgabot
closed
4 years ago
10
Add ska, seqtk to requirements
#23
olgabot
closed
5 years ago
0
Add python3, bam2fasta, update sourmash in environment.yml
#22
olgabot
closed
5 years ago
0
bam2fasta package, process
#21
pranathivemuri
closed
4 years ago
12
Rename extraction of fasta sequences from bam
#20
olgabot
closed
5 years ago
1
Split kmer v2
#19
olgabot
closed
4 years ago
1
Revert "Olgabot/split kmer"
#18
olgabot
closed
5 years ago
0
Extract protein coding sequences before comparing
#17
olgabot
closed
4 years ago
1
Separate outputs by program
#16
olgabot
closed
4 years ago
1
Add fastqc, khtools, move all installation into environment.yml
#15
olgabot
closed
5 years ago
0
Add MultiQC with `sourmash sig describe` on signatures
#14
olgabot
opened
5 years ago
2
add fastp trimming
#13
olgabot
closed
4 years ago
2
Add fastp to container
#12
olgabot
closed
5 years ago
0
Olgabot/add ska to container
#11
olgabot
closed
5 years ago
0
bam file process added in main.nf
#10
pranathivemuri
closed
5 years ago
16
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