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kevinrue
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snakemake_alevin_10x
Snakemake pipeline for 10X using salmon alevin
MIT License
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Use renv to manage a reproducible R environment
#36
kevinrue
opened
4 years ago
0
use tgmap and index generated by pipeline
#35
kevinrue
closed
4 years ago
0
Generate a transcript to gene map
#34
kevinrue
closed
4 years ago
0
Build salmon index
#33
kevinrue
closed
4 years ago
1
Download genome fasta
#32
kevinrue
closed
4 years ago
0
disable conda environment for alevin rule
#31
kevinrue
closed
4 years ago
0
temporary fix: disable conda for `salmon alevin` rule
#30
kevinrue
closed
4 years ago
1
Add rule to generate 'raw' matrix
#29
kevinrue
opened
4 years ago
0
use wildcards instead of params for output folder
#28
kevinrue
closed
4 years ago
0
Apply best practice to write plot
#27
kevinrue
closed
4 years ago
0
Write plots to `results/plots` as per template
#26
kevinrue
closed
4 years ago
0
Add fishpond to bioc conda environment
#25
kevinrue
closed
4 years ago
0
Cleanup
#24
kevinrue
closed
4 years ago
0
Issues
#23
kevinrue
closed
4 years ago
0
symlink FASTQ files in workdir
#22
kevinrue
closed
4 years ago
1
Fix issues
#21
kevinrue
closed
4 years ago
0
Change input file structure to expect all FASTQ files in a single folder
#20
kevinrue
closed
4 years ago
0
Fix issues
#19
kevinrue
closed
4 years ago
0
store rule logs under `results/logs`
#18
kevinrue
closed
4 years ago
0
restore the `results` directory from the template
#17
kevinrue
closed
4 years ago
1
Update schemas for config and sample sheets
#16
kevinrue
closed
4 years ago
0
Explicitly indicate that mem_free is given in GB
#15
kevinrue
closed
4 years ago
0
Issues
#14
kevinrue
closed
4 years ago
0
Parameterise the matching elements of paired reads
#13
kevinrue
closed
4 years ago
0
lint what looks like an absolute path
#12
kevinrue
closed
4 years ago
0
add log directive to rule
#11
kevinrue
closed
4 years ago
0
Separate functions and rule definition in distinct files
#10
kevinrue
closed
4 years ago
0
Document input file structure
#9
kevinrue
closed
4 years ago
0
Document the expected input file structure in README
#8
kevinrue
closed
4 years ago
0
Fixes #1
#7
kevinrue
closed
4 years ago
0
Cleanup
#6
kevinrue
closed
4 years ago
0
use `../scripts/` for rules in `workflow/rules/`
#5
kevinrue
closed
4 years ago
0
use `../envs/` for rules in `workflow/rules/`
#4
kevinrue
closed
4 years ago
0
Integrate first plot to snakemake report
#3
kevinrue
closed
4 years ago
0
Output salmon alevin results in `results/{sample}/salmon`
#2
kevinrue
closed
4 years ago
0
Throw error if no input files are found for any sample
#1
kevinrue
closed
4 years ago
0