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wtsi-team112
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ncov2019-artic-nf
A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019 - adapted to run at the Wellcome Sanger Institute
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Add minReadsPerBarcode parameter for Nanopore workflow
#35
kjsanger
closed
4 years ago
1
Feature/update bam to cram
#34
sb43
opened
4 years ago
13
Remove unnecessary samtools view -bS
#33
ac55-sanger
closed
4 years ago
1
added bamToCram workflow, updated primtertrimmed subflow to emit inde…
#32
sb43
closed
4 years ago
1
added current and failed test in artifacts log
#31
gn5
closed
4 years ago
0
Break use of sanger profile.
#30
sb10
closed
4 years ago
0
upload artifacts
#29
gn5
closed
4 years ago
0
Artifacts upload
#28
gn5
closed
4 years ago
0
Break use of sanger profile.
#27
sb10
closed
4 years ago
0
tests that run on master pull requests
#26
gn5
closed
4 years ago
1
Pull April 3rd upstream changes
#25
sb10
closed
4 years ago
0
Resolve #21 - add docs and changelog
#24
sb10
closed
4 years ago
0
test if Action is triggered
#23
gn5
closed
4 years ago
0
set-up of GitHub Action for tests on develop branch
#22
gn5
closed
4 years ago
0
Document changes and usage of new features
#21
sb10
closed
4 years ago
0
Add CI testing
#20
sb10
closed
4 years ago
9
Switch to development on develop branch, tag master
#19
sb10
closed
4 years ago
4
Output untrimmed bams
#18
roamato
closed
4 years ago
1
Resolve #14 - provide ivar bed and indexed ref file.
#17
sb10
closed
4 years ago
7
Investigate calling quality for Novaseq data
#16
roamato
opened
4 years ago
0
pipe commands for cram to fastq conversion
#15
mgcam
closed
4 years ago
1
Provide own ivar bed file and aligner ref prefix
#14
sb10
closed
4 years ago
2
Work with single ended Illumina data
#13
dkj
opened
4 years ago
1
Resolve isssue #11 - use local schemeRepoURL.
#12
sb10
closed
4 years ago
0
Access schemeRepoURL locally
#11
sb10
closed
4 years ago
5
Resolved issue #9 - corrected --cram option requiring trailing slash
#10
JonKeatley112
closed
4 years ago
0
`--cram` option requires a trailing `/` after the directory
#9
roamato
closed
4 years ago
0
close #6
#8
roamato
closed
4 years ago
0
Issue3 cramtofastq
#7
JonKeatley112
closed
4 years ago
0
Change default to V2 primers and ligation setup
#6
roamato
closed
4 years ago
0
solves #1
#5
roamato
closed
4 years ago
0
Rename input files to match sample names
#4
roamato
closed
4 years ago
3
Integrate carm->fastq conversion step
#3
roamato
closed
4 years ago
0
Access singularity image in a different path
#2
roamato
closed
4 years ago
1
Add support for LSF
#1
roamato
closed
4 years ago
0