Template/update #133
Template/update #133
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it might make sense to create a new branch off of |
CHANGELOG.md
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| @@ -26,6 +27,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | |||
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| - [#132](https://github.com/mskcc/forte/pull/132) - fix generate cff split/span logic for fusioncatcher and arriba | |||
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| - [#133](https://github.com/mskcc/forte/pull/133) - Template update for nf-core/tools v3.1.1 | |||
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i elaborated a bit more. since the PR is linked someone can always follow the link to get more information.
nextflow.config
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| // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 | ||
| [ | ||
| name: 'Anne Marie Noronha', | ||
| affiliation: '', |
| @@ -11,7 +11,7 @@ workflow GROUP_READS { | |||
| def fastq_pair_id = meta.fastq_pair_id | |||
| def meta_clone = meta.clone().findAll { !["read_group","fastq_pair_id"].contains(it.key) } | |||
| meta_clone.id = meta.sample | |||
| [groupKey(meta_clone,meta.fq_num), reads, read_group, fastq_pair_id] | |||
| [meta_clone, reads, read_group, fastq_pair_id] | |||
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Don't need fq_num anymore? is it in the meta_clone item now?
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i think i was struggling to find a place for fq_num because the input sheet workflow changed so much. either way I don't think it's necessary because without groupKey it should still group the correct number of fastqs anyways? It would make sense to add back if we were using something like watchPath, i believe.
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why was this deleted?
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after I updated nextflow to work with this branch, something is wrong with the baits file now? error I'm getting
Curious if its something to do with the change ifrom having params in getGenomeAttribute to removing it in this: Line 22 in db0c18f |
| @@ -208,6 +204,8 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof | |||
| - A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) | |||
| - `apptainer` | |||
| - A generic configuration profile to be used with [Apptainer](https://apptainer.org/) | |||
| - `wave` | |||
| - A generic configuration profile to enable [Wave](https://seqera.io/wave/) containers. Use together with one of the above (requires Nextflow ` 24.03.0-edge` or later). | |||
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I think in the readme we should explicitly state that the version of nextflow must be 24.03.0 or later.
Pipeline template update
Some well overdue pipeline template updates. Because there hasn't been a sync in so long i had to follow the sync retrospectively guide, but now that we are in sync we should in the future be able to follow the manual sync guide, provided we don't wait too long between updates.
Some highlights in the update:
assets/schema_input.json. The maf input file is also now validated using nf-schema using a separate definition fileassets/schema_maf_input.json.I am also switching the main development branch to
devso as to more closely reflect the pipeline and avoid discordance with future template syncs. All github actions triggering withdevelopshould now trigger withdev, and the base branch of PRs should bedev, unless the PR fordevto be merged intomainPR checklist
nf-core lint).nextflow run . -profile 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).