initial pipeline pseudo PR #17
Draft
+7,972
−151
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Createtsv tests
Chunking clusters
…a tags updated to chunk level
…r post-processing
exporting reps to fams mapping and fasta
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
… optional directory parameters added to output.md
…sholds changed to 0.97
Review points from James
first release version bump (1.0.0)
jfy133
reviewed
Feb 5, 2025
CHANGELOG.md
Outdated
| @@ -3,14 +3,16 @@ | |||
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | |||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | |||
|
|
|||
| ## v1.0.0dev - [date] | |||
| ## v1.0.0 - [2025/02/03] | |||
There was a problem hiding this comment.
Suggested change
| ## v1.0.0 - [2025/02/03] | |
| ## v1.0.0 - [2025/02/05] |
| @@ -31,6 +463,10 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d | |||
|
|
|||
| Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>. | |||
|
|
|||
| Custom output MultiQC data includes a metadata file (multiqc_data/multiqc_family_metadata.txt) with family information such as: Sample,Family Id,Size,Representative Length,Representative Id,Sequence | |||
There was a problem hiding this comment.
Suggested change
| Custom output MultiQC data includes a metadata file (multiqc_data/multiqc_family_metadata.txt) with family information such as: Sample,Family Id,Size,Representative Length,Representative Id,Sequence | |
| Custom output MultiQC data includes a metadata file (`multiqc_data/multiqc_family_metadata.txt`) with family information such as: Sample,Family Id,Size,Representative Length,Representative Id,Sequence |
|
|
||
| // Check if base filenames match one to one | ||
| if (baseNames1 != baseNames2) { | ||
| error("Filename mismatch: Expected matching files in ${folder1} and ${folder2}. Base filenames do not match.") |
There was a problem hiding this comment.
Suggested change
| error("Filename mismatch: Expected matching files in ${folder1} and ${folder2}. Base filenames do not match.") | |
| error("nf-core/proteinfamilies] ERROR: Filename mismatch: Expected matching files in ${folder1} and ${folder2}. Base filenames do not match.") |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).