topics bismark/align #9272
Merged
topics bismark/align #9272
Conversation
This file contains hidden or 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
maxulysse
reviewed
Oct 28, 2025
Comment on lines
105
to
106
| "bismark", | ||
| " Bismark - Bisulfite Mapper and Methylation Caller.\n\n0.25.1\n \n https://github.com/FelixKrueger/Bismark" |
Member
There was a problem hiding this comment.
too much info captured I'm afraid
mashehu
pushed a commit
that referenced
this pull request
Nov 20, 2025
* topics bismark/align * fix versions command --------- Co-authored-by: Marcel Ribeiro-Dantas <[email protected]>
github-merge-queue bot
pushed a commit
that referenced
this pull request
Nov 28, 2025
* topics bismark/align (#9272) * topics bismark/align * fix versions command --------- Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> * Converts FASTQ to use topics for version (#9266) * Converts FASTQ to use topics for version Fixes #9261 * Updates meta.yml file * Updates snapshot * Update modules/nf-core/fastqc/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/fastqc/meta.yml Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Updates snapshot * Removes .mix versions of FASTQ in subworkflows * Updates snapshots of fastqc modules and related subworkflows * Updates snapshots of fastqc * Updates fastqc snapshot * Sanitizes process.out for indexed outputs * Updates fastqc snapshot * Updates fastqc snapshot * Adds topic to the meta.yml file * Fixes syntax usage of topic * Adds new Devcontainer Setup for use with Codespaces (#8983) * Add devcontainer setup from nf-core/tools for testing. Move nf-test install to setup.sh * Add the default user again at the end * Move nf-test install to unprivileged location and add WORKDIR. Add pipefail. Remove copying unnecessary files. * Move Dockerfile * Remove docker-in-docker interfering with docker-outside-docker from parent image. Adapt Mounts to use host paths when starting sibling containers * Fix arm profile * Remove apptainer install * Remove efforts for unprivileged user * Use root user by default * update welcome message. update prompt * Remove explicitly setting NFT_WORKDIR * Add nf-test as local feature * Remove Dockerfile in favor of features * Remove env vars * Add apptainer as local feature * Fix install * Fix install script for apptainer by installing dependencies first * Fix install script for apptainer by installing dependencies first * Update local feature to have version, name, id * ftr: new devcontainer config * Remove redundant tools install * Remove local features. Already installed in parent image * Testing: Change to pulling image from controlled location for testing in codespaces. REVERT THIS * fix: set executable bit flag to run setup.sh * Change to final container image * Bumpy hostRequirements to run in more powerful instance in Codespaces * Switch to using dev tag of our nf-core/devcontainer * Fixes meta.yml file indenting + syntax * Fixes meta.yml with nf-core modules lint fastqc --fix * Removes accidental adding of .devcontainer * Fixes null version in subworkflow snapshot --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: JulianFlesch <[email protected]> # Conflicts: # .devcontainer/devcontainer.json * Multiqc2topics (#9271) * update multiqc to use topics for versions * update nf-test and snapshots * update meta.yml * update main.nf.test after review * removed and re-generated main.nf.test.snap after changes * Fixing remarks * Fix failing linting tests --------- Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> * Add Topic-based tool version capture to Trinity Module (#9273) * add versions topic to trinity module * add missing test for main.nf.test * simplify string replacement for trinity version eval to remove use of colons - avoids potential yml clash * update meta.yml to capture new version topics change * add new test for aggregating versions via topic * update snapshot for new tests * Update modules/nf-core/trinity/meta.yml remove leading space Co-authored-by: Nicolas Vannieuwkerke <[email protected]> --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * adding topics channel to tabix_tabix (#9267) * adding topics channel * nf-test * lint meta yml * redo meta.yml * remove dup * remove tabix version * remove tabix versions from subworkflows * fix test * update snapshot * fix snapshots subworkflows * missed one subworkflow * more subworkflows * last (?) subworkflow * harshils alignmnent * too enthusiatic when removing * snaphots because bgzip versions are back * fix topics syntax for linting * Revert "fix topics syntax for linting" This reverts commit 0d25630. * version syntax changed in test * remove newline * Update modules/nf-core/tabix/tabix/main.nf Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Update modules/nf-core/tabix/tabix/meta.yml Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * snapshot for new version_tabix name --------- Co-authored-by: mapo9 <[email protected]> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: Nicolas Vannieuwkerke <[email protected]> * Topics/samtools view (#9301) * topics bamstats generalstats * fix version * update samtools/view to use topics * feat: update samtools sort module with version topic support (#9275) * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * feat: update samtools sort module with version topic support * Update meta.yml and test snapshot * remove .devcontainer * Revert "remove .devcontainer" This reverts commit a97a7a2. --------- Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> * feat: update samtools stats module with version topic support (#9330) * Adds version topic channel to SAMTOOLS_STATS * Removes version mix in subworkflow * Removes version mix for samtools sort * Updates snapshots for tests * Update modules/nf-core/samtools/stats/main.nf Co-authored-by: Simon Pearce <[email protected]> * Update modules/nf-core/samtools/stats/meta.yml Co-authored-by: Simon Pearce <[email protected]> * Fixes meta.yml * [automated] Update gpu snapshot * [automated] Update gpu snapshot * remove accidentally added file --------- Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: nf-core-bot <[email protected]> Co-authored-by: mashehu <[email protected]> * [automated] Update gpu snapshot * update snapshot * fix new topics structure * fix pre-commit * fix bam_split_by_region linting * fix fastq_align snapshots * update snapshots * remove references for FASTQC.out.versions * fix linting for fastq_align_chromap * update snapshots * remove old version channel for samtools/sort * fix fastq_create_umi_consensus_fgbio snapshot * fix fastq_align_star snapshots * fix id in snapshot * update vcf_gather_bcftools snapshot * update vcf_annotate_ensemblvep snapshot * fix snapshot --------- Co-authored-by: Nicolas Vannieuwkerke <[email protected]> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: JulianFlesch <[email protected]> Co-authored-by: Kobe Lavaerts <[email protected]> Co-authored-by: eit-maxlcummins <[email protected]> Co-authored-by: Mark Polster <[email protected]> Co-authored-by: mapo9 <[email protected]> Co-authored-by: wangyang <[email protected]> Co-authored-by: Marcel Ribeiro-Dantas <[email protected]> Co-authored-by: Simon Pearce <[email protected]> Co-authored-by: nf-core-bot <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
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
Closes #XXX
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda