issues
search
Arcadia-Science
/
seqqc
A Nextflow pipeline to identify quality control issues with new sequencing data.
MIT License
27
stars
0
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
small changes from dev -> master for release
#45
taylorreiter
closed
1 year ago
1
quick PR for changes before release
#44
taylorreiter
closed
1 year ago
1
email changes from dev to master
#43
taylorreiter
closed
1 year ago
1
Move away from nf-core-modified
#42
mertcelebi
opened
1 year ago
0
Fix all email notifications
#41
mertcelebi
closed
1 year ago
1
process CUSTOM_DUMPSOFTWAREVERSIONS uses multiqc 1.13, but multiqc uses multiqc 1.14
#40
taylorreiter
closed
1 year ago
1
two versions of wget in download mod
#39
taylorreiter
closed
1 year ago
1
Cron job & email template
#38
taylorreiter
closed
1 year ago
1
Add the services config for email notification secrets
#37
mertcelebi
closed
1 year ago
1
Fix the cron job by changing the env variable name + the working dir
#36
mertcelebi
closed
1 year ago
1
add workflow dispatch to the cron job config to enable manual triggers
#35
mertcelebi
closed
1 year ago
1
Deduplicate AWS Tower full test github actions workflows
#34
taylorreiter
opened
1 year ago
1
Move nf-core-modified out of local for better visual hierarchy
#33
mertcelebi
closed
1 year ago
5
Daily cron job for triggering seqqc runs across Arcadia
#32
mertcelebi
closed
1 year ago
3
Clean up to do strings, citations, methods, changelog and readme in prep for release 1
#31
taylorreiter
closed
1 year ago
1
Enable singularity
#30
taylorreiter
closed
1 year ago
1
enable retries upon job failure to increase resources automatically. Also bump nextflow version and conda declarations to nf-core latest
#29
taylorreiter
closed
1 year ago
4
draft of data upload instructions for cron job
#28
taylorreiter
closed
1 year ago
0
Make arcadia branch that contains arcadia-specific explanations and text
#27
taylorreiter
opened
1 year ago
0
Tower run on isoseq full test data set fails
#26
taylorreiter
closed
1 year ago
1
update email template with instructions for multiqc report
#25
taylorreiter
closed
1 year ago
2
remove the sourmash contamination database from the publish dir?
#24
taylorreiter
opened
1 year ago
0
start files for full test on tower via aws batch
#23
taylorreiter
closed
1 year ago
3
create a tower.yml file so that that multiqc report will show up in tower
#22
taylorreiter
closed
1 year ago
4
Swap out the test data set for one that will produce sourmash gather results and has long read data
#21
taylorreiter
closed
1 year ago
2
Update email template
#20
taylorreiter
closed
1 year ago
1
Update multiqc container to biocontainer when sourmash PRs are merged and there is a new release of multiqc
#19
taylorreiter
opened
1 year ago
0
Including sourmash taxonomy annotate in seqqc
#18
taylorreiter
opened
1 year ago
0
Update documentation for pipeline
#17
taylorreiter
closed
1 year ago
2
update workflow to ingest sourmash outputs, update multiqc docker container
#16
taylorreiter
closed
1 year ago
3
documenting creation of temporary multiqc docker image for sourmash reporting.
#15
taylorreiter
opened
1 year ago
8
probably not a good idea to contain SRR accessions in the database
#14
taylorreiter
closed
1 year ago
1
Setting the pipeline up to work with long read data
#13
taylorreiter
closed
1 year ago
1
Test data for long read data
#12
elizabethmcd
closed
1 year ago
1
Expectations for how long-reads will be QCed and implemented with this workflow
#11
elizabethmcd
closed
1 year ago
1
Add sourmash compare module to workflow
#10
taylorreiter
closed
1 year ago
1
building a contamination database that is small so it downloads and runs quickly
#9
taylorreiter
closed
1 year ago
2
add workflow for gather
#8
taylorreiter
closed
1 year ago
2
from dev to master for release 1
#7
taylorreiter
closed
1 year ago
1
add modules, change test data set, and ignore outpute
#6
taylorreiter
closed
1 year ago
0
documenting getting started with nf-core create
#5
taylorreiter
opened
1 year ago
2
Turn the nf-core modules into a workflow: sourmash sketch & sourmash gather
#4
taylorreiter
closed
1 year ago
1
nextflow run on main branch
#3
elizabethmcd
closed
1 year ago
1
Remove `params.fasta` since this should work on fastq data
#2
taylorreiter
closed
1 year ago
5
add current sourmash modules
#1
taylorreiter
closed
1 year ago
0