Skip to content

Metagenomics Illumina NF conversion and pipeline update #152

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 56 commits into from
May 8, 2025
Merged

Metagenomics Illumina NF conversion and pipeline update #152

merged 56 commits into from
May 8, 2025

Conversation

bnovak32
Copy link
Contributor

@bnovak32 bnovak32 commented May 8, 2025

Pipeline updates:

  • The following tool versions were updated:
    • FastQC
    • MultiQC
    • bowtie2
    • samtools
    • CAT
    • GTDB-Tk
    • HUMAnN
    • MetaPhlAn
  • In step 14d, MAG taxonomic classification, added the new --skip_ani_screen argument to gtdbtk classify_wf to continue classifying genomes as in previous versions of GTDB-Tk, using mash and skani.

Workflow updates:

olabiyi and others added 30 commits May 1, 2024 15:16
@olabiyi
first commit
95b29a7
@olabiyi
Added Documentation
ca431fc
@olabiyi
fixed params.conda
d4fcd12
@olabiyi
Fixed paths and executor issues
f239d0e
@olabiyi
Limited queue size
2bb8049
@olabiyi
Enabled retrial of failed processes
ea51ab3
@olabiyi
Edited container engine variable
9f07478
@olabiyi
Handled pyfastx fasta index error
deea523
@olabiyi
Now accepts GLDS accessions
6e68d0e
@olabiyi
fix GTDBTK download
e409a28
@olabiyi
Fixed humann utilities mounting issue
72b0601
@olabiyi
Edited software collation
a4df49d
@olabiyi
Updated GTDBTK
d2cfbdf
@olabiyi
Added README.md
5b5cfa3
@olabiyi
Fixed extra header issue
f299748
@olabiyi
Fixed GTDBTK taxonomy variable issue
d119d4c
@olabiyi
Changed default database location
9b79149
@olabiyi
Updated versions and README
6409cbf
@olabiyi
fixed README typo
c750589
@olabiyi
fixed README typo
c6c929a
@olabiyi
fixed README typo
54effb8
@asaravia-butler
Merge pull request #101 from olabiyi/DEV_Metagenomics_Illumina_NF_con…
255744d 
…version

Metagenomics Illumina Nextflow workflow
@asaravia-butler
Updating header and correcting tool version typos
8e36cc8
@asaravia-butler
Adding updates from previous version
b9e234b
@bnovak32
Update GL-DPPD-7107-A.md
42b723a 
Changed text in "updates" section to more clearly explain the change in step 14d and fixed the capitalization on the GTDB-Tk software package.
@asaravia-butler
Merge pull request #116 from bnovak32/DEV_Metagenomics_Illumina_NF_co…
88739e0 
…nversion

Update description of changes
@asaravia-butler
Updating change description
9a232e6
@olabiyi
Added post-processing workflow
9dfa6fa
@asaravia-butler
Typo fixes
0279deb
@asaravia-butler
Typo fixes
ba86dc5
bnovak32 and others added 26 commits September 11, 2024 10:59
@bnovak32
Update GL-DPPD-7107-A.md
28843a3 
- minor changes to software names in table (to match capitalization in each tool's documentation)
- updated mutliqc commands to remove "-z" option which is not used in any workflows
- updated thread specifications to use generic "NumerOfThreads" rather than specific number.
@asaravia-butler
Merge pull request #121 from bnovak32/patch-4
5adb13f 
MultiQC correction, typo fixes
@olabiyi
Merge branch 'nasa:DEV_Metagenomics_Illumina_NF_conversion' into DEV_…
34b63a7 
…Metagenomics_Illumina_NF_conversion
@asaravia-butler
Merge pull request #117 from olabiyi/DEV_Metagenomics_Illumina_NF_con…
ecb72e8 
…version

Metagenomics Nextflow workflow: Added post-processing workflow
@asaravia-butler
Adding notes.
0c85354
@asaravia-butler
Typo fix
e5110cb
@asaravia-butler
Adding missing pipeline info
c3ca4ed
@asaravia-butler
Version info updates
d2f33dd
@asaravia-butler
Formatting update
11d1dbd
@asaravia-butler
renaming NF_MGIllumina to NF_MGIllumina-A
cfdd9a7
@olabiyi
Edited README and accession parameter
e5c4fe6
@olabiyi
minor README edit
da5d9db
@asaravia-butler
Merge pull request #127 from olabiyi/DEV_Metagenomics_Illumina_NF_con…
f34870c 
…version

Metagenomics Illumina Nextflow workflow: Edited README files and accession parameter
@olabiyi
renamed accession parameter
b03f9ad
@asaravia-butler
Updatign signature matrix
1aeeb73
@asaravia-butler
Updating nextflow version
59b1653
@asaravia-butler
Formatting updates
54c5bd8
@asaravia-butler
Formatting updates
0dcec9b
@olabiyi
Merge branch 'nasa:DEV_Metagenomics_Illumina_NF_conversion' into DEV_…
ca89a74 
…Metagenomics_Illumina_NF_conversion
@olabiyi
Fixed read mapping bug
311800e
@olabiyi
Fixed typos and no assemblies produced bug
e91d7a5
@asaravia-butler
Merge pull request #129 from olabiyi/DEV_Metagenomics_Illumina_NF_con…
703f469 
…version

Nextflow Metagenomics Illumina conversion: Added missing post-processing script and fixed no assemblies produced bug
@olabiyi
Metagenomics Illumina Nextflow conversion (#134)
620598f 
* improved checkm performance by running separately on every bin
* fixed typo in config
* updated the nextflow version
* changed the default value of accession input parameter
* reverted AmpIllumina pipeline doc to remove updates
* added launchDir variable
* made format changes to config files
* updated README
* updated MGIllumina pipeline doc after CCB approval
* added launch scripts and fixed bugs
* deleted cluster path
* fixed humman utilities mounting bug
* commented out singularity cache_dir
* updated the content of processing_info.zip to match other GeneLab Nextflow workflows
@bnovak32
Updated documentation (#150)
2a16111 
- Updated Pipeline doc
    - added missing output files for assembly based processing
    - added links between steps for file references
    - fixed step references
- Created examples/runsheet folder for CSV examples files
	- Added runsheet documentation
- Updated ChangeLog
   - added ChangeLog documentation
   - reformatted references to pipeline and previous snakemake workflow
   - added closed issue references
   - added other workflow specific updates vs previous snakemake
     workflow (checkm implementation)
- Updated Workflow README
   - add docker references since both Docker and Singularity are
     supported
   - regularize capitalization of Nextflow and Singularity to match
     the tools' documentation
   - reorganize post-processing output definition to match other assays
   - clarify installation instructions for conda in workflow document
- Added missing assay suffix to "Failed" assembly file name
- Rename NF_MGIllumina-A to NF_MGIllumina
- Checked and updated all broken links
@bnovak32
[DEV_Metagenomics_Illumina] Minor documentation updates (#151)
f9dec7c 
- Pipeline doc
  - fixed typo in sed command
- NF workflow doc
  - added explicit definitions for all profiles available
  - removed slurm from example command-line calls
  - updated headings to adjust slurm removal
- simplified instructions for different run approaches
- added conda env configuration information as additional information under the conda profile definition.
@bnovak32
revert permissions on SW_MGIllumina scripts
eee1c4c
@bnovak32 bnovak32 merged commit 296943b into master May 8, 2025
0 of 2 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@bnovak32 @olabiyi @asaravia-butler