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Mgnify amplicon pipeline #658

Merged
merged 9 commits into from
Feb 3, 2025
Merged

Mgnify amplicon pipeline #658

merged 9 commits into from
Feb 3, 2025

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RZ9082
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@RZ9082 RZ9082 commented Jan 27, 2025

FOR CONTRIBUTOR:

  • I have read the Adding workflows guidelines
  • License permits unrestricted use (educational + commercial)
  • Please also take note of the reviewer guidelines below to facilitate a smooth review process.

FOR REVIEWERS:

  • .dockstore.yml: file is present and aligned with creator metadata in workflow. ORCID identifiers are strongly encouraged in creator metadata. The .dockstore.yml file is required to run tests
  • Workflow is sufficiently generic to be used with lab data and does not hardcode sample names, reference data and can be run without reading an accompanying tutorial.
  • In workflow: annotation field contains short description of what the workflow does. Should start with This workflow does/runs/performs … xyz … to generate/analyze/etc …
  • In workflow: workflow inputs and outputs have human readable names (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless it is generally understood. Altering input or output labels requires adjusting these labels in the the workflow-tests.yml file as well
  • In workflow: name field should be human readable (spaces are fine, no underscore, dash only where spelling dictates it), no abbreviation unless generally understood
  • Workflow folder: prefer dash (-) over underscore (_), prefer all lowercase. Folder becomes repository in iwc-workflows organization and is included in TRS id
  • Readme explains what workflow does, what are valid inputs and what outputs users can expect. If a tutorial or other resources exist they can be linked. If a similar workflow exists in IWC readme should explain differences with existing workflow and when one might prefer one workflow over another
  • Changelog contains appropriate entries
  • Large files (> 100 KB) are uploaded to zenodo and location urls are used in test file

@RZ9082
amplicon subworkflows
536e897 
add .dockstore.yml

update trimmomatic suffix

update trimmomatic revision

update workflows

updated PE and SE tests

updated PE and SE tests

add workflow to test query_tabular input

add workflow to test query_tabular input

add workflow to test query_tabular input

update test query_tabular

update test query_tabular

updated cmsearch-deoverlap

update cmsearch-deoverlap

remove testing-query-tabular

update after-quality-control tests

update after-quality-control tests

add annotations to the post-QC sub-WF

updated input names

add annotations

typo in the annotation

update PE-WF annotation

typo

update QC annotations

add README files

split post-QC sub-WF & create a complete WF

delete old post-QC sub-WF

adding dockstore files

update mapseq-DB IDs

update tests

add summary tables sub-WF

update QC tests

add annotation and license to summery tables sub-WF

added READMEs

update seqprep in PE sub-WF

hide mid-steps, add input parameter for summary table names

ITSonedb --> ITSoneDB

added summary-tables-swf to complete wf

fastq-dump --> fasterq-dump & test updates

del not used test files

add delta values to tests

has_n_lines

first line in summary tables was missing

add mapseq-to-ampvis2 WF

filter empty datasets

update mapseq-to-ampvis2/.dockstore.yml

update QC tests

update ampvis test

update WF-names & add conditions for col-join, krona, and biom-convert

del old WFs

adjust ssu summ test

set fasta width to 60 in PE sub-WF

update PE QC processed fasta test-file

add zenodo link & remove test files

move workflows to dedicated folder

add taxonomic rank abundane summary table workflow

apply review suggestions

add release to WFs

add missing quotation mark

replace fasterq-dump with fastq-dl, formatting, and updating tests
@RZ9082
test using CM file from history
98f808c
@RZ9082
try cmsearch v1.1.5 using cached CM file
de6b422
@RZ9082
update cmsearch to v1.1.5
99ef72d
@RZ9082
update labels for SE
18688a8
@RZ9082
update labels and tool versions in ITS WF
217352e
@RZ9082
update labels and tool versions in PE WF
cf2342a
@RZ9082
update labels and tool versions in rRNA-prediction WF
597ae96
@RZ9082
Updated names and updated MultiQC version
2439102
@bgruening bgruening merged commit f1b7d92 into galaxyproject:main Feb 3, 2025
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@bgruening
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Thanks @RZ9082. Thanks for constantly working on this and getting it ready!!!!

@RZ9082
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RZ9082 commented Feb 3, 2025

Thanks @RZ9082. Thanks for constantly working on this and getting it ready!!!!

Thanks for the support!

@mvdbeek
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mvdbeek commented Feb 3, 2025

Indeed, thanks a lot @RZ9082!

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@bgruening bgruening bgruening approved these changes

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3 participants
@RZ9082 @bgruening @mvdbeek