naobservatory/mgs-workflow

Issues

• Implement fragment-length analysis

  #57 opened a month ago by willbradshaw
  1

• Implement duplication analysis

  #56 opened 2 months ago by willbradshaw
  1

• Change repo name to mgs-pipeline-v2?

  #6 opened 6 months ago by mikemc
  6

• Consider adding a check that the required files are present at the start of the workflow

  #23 opened 2 months ago by mikemc
  1

• Error checking in concat_gzipped

  #45 opened 2 months ago by evanfields
  2

• Improve reference DB for viral detection pipeline

  #55 opened 2 months ago by willbradshaw
  0

• Automate logging and include in publish directory

  #54 opened 2 months ago by willbradshaw
  0

• Fix deduplication issues for unmerged read pairs

  #53 opened 2 months ago by willbradshaw
  0

• Cut down working and output directories

  #52 opened 2 months ago by willbradshaw
  0

• Auto-scale process resources

  #51 opened 2 months ago by willbradshaw
  0

• Identify and eliminate runtime bottlenecks

  #50 opened 2 months ago by willbradshaw
  0

• Restructure sample sheet and eliminate CONCAT_GZIPPED

  #49 opened 2 months ago by willbradshaw
  0

• Consider marking duplicates in bowtie2 HV output with `samtools markdup`

  #48 opened 3 months ago by mikemc
  3

• Consider moving scripts from bin/ to their corresponding module

  #47 opened 3 months ago by mikemc
  1

• join_fastq is a bit of a bottleneck

  #44 opened 3 months ago by evanfields
  6

• Consider adapter trimming just from 3' end

  #43 opened 3 months ago by mikemc
  1

• QC on undefined channel in RAW workflow (only when subsampling reads)

  #42 opened 2 months ago by evanfields
  1

• Math in footnote 8 doesn't render correctly.

  #39 opened 2 months ago by simonleandergrimm
  4

• Respect given memory parameter in BBTools processes

  #36 opened 4 months ago by mikemc
  7

• Standardized metadata

  #19 opened 2 months ago by jeffkaufman
  10

• Refine treatment of partially-HV taxa

  #35 opened 4 months ago by willbradshaw
  1

• Make peri-dedup taxonomic profiling optional

  #34 opened 2 months ago by willbradshaw
  1

• Handling reverse-complement duplicates in paired reads

  #30 opened 2 months ago by mikemc
  5

• Adding instructions for running with limited cpus and/or memory

  #29 opened 4 months ago by mikemc
  4

• SDKMAN! dependency

  #28 opened 2 months ago by mikemc
  2

• `GET_HV_DESCENDENTS` is very slow

  #27 opened 5 months ago by willbradshaw
  4

• Adding `addcount=t` to clumpify call in dedup step

  #26 opened 2 months ago by mikemc
  5

• Is importing data into S3 in-scope for this project?

  #25 opened 2 months ago by jeffkaufman
  1

• Add explicit tracking of pathogens of interest

  #20 opened 5 months ago by willbradshaw
  1

• Update MultiQC version

  #18 opened 6 months ago by willbradshaw
  1

• Adding a description of the pipeline to the repo

  #5 opened 6 months ago by mikemc
  4

• EXTRACT_UNCONC_READS is too slow

  #10 opened 2 months ago by willbradshaw
  4

• Institute a changelog?

  #9 opened 2 months ago by mikemc
  4

• Suggestions for documenting files

  #8 opened 6 months ago by mikemc
  3

• Saving additional information for reproducibility

  #32 opened 4 months ago by willbradshaw
  1

• Change containers to specific versions

  #33 opened 4 months ago by willbradshaw
  1

• Improve flexibility of input files

  #16 opened 6 months ago by willbradshaw
  5

• Implement nf-core best practices

  #13 opened 6 months ago by willbradshaw
  2

• Options for allowing more diverse read names

  #24 opened 5 months ago by mikemc
  2

• Try removing reference copying steps

  #22 opened 5 months ago by willbradshaw
  5

• Add profiles for different run settings

  #21 opened 5 months ago by willbradshaw
  2

• Fixing numbering of workflow steps (or remove numbering)

  #15 opened 5 months ago by mikemc
  4

• Move scripts to bin directory

  #14 opened 5 months ago by willbradshaw
  1

• Add more files to results folder

  #12 opened 5 months ago by willbradshaw
  2

• Many reference databases are out of date

  #11 opened 5 months ago by willbradshaw
  1

• Possibly erroneous comment above process BOWTIE2_INDEX_REFERENCES

  #7 opened 5 months ago by mikemc
  1

• main.config is pointing to `ref/adapters.fa`, but the file is called `ref/adapters.fasta`

  #4 opened 5 months ago by simonleandergrimm
  1

• nextflow.config defines script_dir path as script_dir = "${projectDir}/../repo/scripts/" but "repo" should either be mgs-workflow or a variable.

  #1 opened 5 months ago by simonleandergrimm
  1

• Where is the code that produces `kraken_reports.tsv.gz`?

  #17 opened 6 months ago by mikemc
  1

• arb-silva data is not available anymore.

  #2 opened 7 months ago by simonleandergrimm
  3