naobservatory mgs-workflow issues

naobservatory / mgs-workflow

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issues

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`GET_HV_DESCENDENTS` is very slow

#27 willbradshaw opened 5 days ago
3
Adding `addcount=t` to clumpify call in dedup step

#26 mikemc opened 1 week ago
1
Is importing data into S3 in-scope for this project?

#25 jeffkaufman opened 1 week ago
1
Options for allowing more diverse read names

#24 mikemc closed 5 days ago
2
Consider adding a check that the required files are present at the start of the workflow

#23 mikemc opened 1 week ago
0
Try removing reference copying steps

#22 willbradshaw closed 5 days ago
5
Add profiles for different run settings

#21 willbradshaw closed 5 days ago
2
Add explicit tracking of pathogens of interest

#20 willbradshaw opened 3 weeks ago
0
Standardized metadata

#19 jeffkaufman opened 4 weeks ago
8
Update MultiQC version

#18 willbradshaw opened 1 month ago
1
Where is the code that produces `kraken_reports.tsv.gz`?

#17 mikemc closed 1 month ago
1
Improve flexibility of input files

#16 willbradshaw opened 1 month ago
4
Fixing numbering of workflow steps (or remove numbering)

#15 mikemc closed 5 days ago
4
Move scripts to bin directory

#14 willbradshaw closed 5 days ago
1
Implement nf-core best practices

#13 willbradshaw opened 1 month ago
2
Add more files to results folder

#12 willbradshaw closed 5 days ago
2
Many reference databases are out of date

#11 willbradshaw closed 5 days ago
1
EXTRACT_UNCONC_READS is too slow

#10 willbradshaw opened 1 month ago
3
Institute a changelog?

#9 mikemc opened 1 month ago
3
Suggestions for documenting files

#8 mikemc opened 1 month ago
2
Possibly erroneous comment above process BOWTIE2_INDEX_REFERENCES

#7 mikemc closed 5 days ago
1
Change repo name to mgs-pipeline-v2?

#6 mikemc opened 1 month ago
2
Adding a description of the pipeline to the repo

#5 mikemc opened 1 month ago
3
main.config is pointing to `ref/adapters.fa`, but the file is called `ref/adapters.fasta`

#4 simonleandergrimm closed 5 days ago
1
Changed repo to mgs-workflow in the definition of three paths in index.config to be consistent with the name the repo has.

#3 simonleandergrimm closed 1 month ago
2
arb-silva data is not available anymore.

#2 simonleandergrimm closed 2 months ago
3
nextflow.config defines script_dir path as script_dir = "${projectDir}/../repo/scripts/" but "repo" should either be mgs-workflow or a variable.

#1 simonleandergrimm closed 5 days ago
1