Merge modules with new topics syntax #9333
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* topics bismark/align * fix versions command --------- Co-authored-by: Marcel Ribeiro-Dantas <marcel.ribeirodantas@seqera.io>
* 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 <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/fastqc/meta.yml Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * 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 <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: JulianFlesch <julianflesch@googlemail.com>
* 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 <marcel.ribeirodantas@seqera.io>
* 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 <101190534+nvnieuwk@users.noreply.github.com> --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
* 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 <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/tabix/tabix/meta.yml Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * snapshot for new version_tabix name --------- Co-authored-by: mapo9 <mark.poslter@qbic.uni-tuebingen.de> Co-authored-by: Marcel Ribeiro-Dantas <marcel.ribeirodantas@seqera.io> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>
* topics bamstats generalstats * fix version * update samtools/view to use topics
* 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 <marcel@seqera.io> Co-authored-by: Marcel Ribeiro-Dantas <marcel.ribeirodantas@seqera.io>
* 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 <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/samtools/stats/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fixes meta.yml * [automated] Update gpu snapshot * [automated] Update gpu snapshot * remove accidentally added file --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: mashehu <mashehu3@gmail.com>
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@nf-core-bot update snapshot path: subworkflows/nf-core/fastq_align_bowtie2 |
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@nf-core-bot update snapshot path: subworkflows/nf-core/bam_split_by_region |
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See https://deploy-preview-3613--nf-core-main-site.netlify.app/blog/2025/version_topics for details about this effort