chipseq
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nf-core
ChIP-seq peak-calling, QC and differential analysis pipeline.
### Description of feature See [this](https://github.com/nf-core/chipseq/pull/413#discussion_r1781213843) comment and thread on this comment on the PR to release 2.1.0 (#413)
### Description of feature Probably [this](https://github.com/JoseEspinosa/nf-core-chipseq/blob/686c054c33ec1606aa05d2347460994dfa2cd618/workflows/chipseq.nf#L432-L438) could be moved to the prepare_genome subworkflow.
### Description of feature As requested [here](https://github.com/nf-core/atacseq/pull/371#pullrequestreview-2158763937), the pipeline should switch to nf-schema. As the validation needs to use features of nf-schema and the current template still uses nf-validation, this...
The primary change addresses GitHub issue #468. In `modules/local/bedtools_genomecov.nf`, the `bedtools genomecov` command was updated from `-bg` to `-bga`. This ensures bigWig files include zero-coverage bins, resulting in lower background...
### Description of the bug We have observed an interesting behaviour when it comes to the bigWig file generation in both the ChIP-seq as well as CUT&RUN workflow, and I...
### Description of feature # Description Currently, the [bedtools_genomecov](https://github.com/nf-core/chipseq/blob/51eba00b32885c4d0bec60db3cb0a45eb61e34c5/modules/local/bedtools_genomecov.nf) module is implemented as a local module. There is however an nf-core module for it https://nf-co.re/modules/bedtools_genomecov. The local module should probably...
### Description of the bug **Background** Akin to the exact same error behaviour and outcome to a related issue here: https://github.com/nf-core/chipseq/issues/440#issue-2741780891: We have metadata from a large scale plant chipseq...
### Description of feature If there is not chip-seq input control, then the pipeline does not call peaks by macs3. It is hard to find input control on ncbi. It...
### Description of the bug Error trying to run the workflow in test mode when using singularity. ### Command used and terminal output ```console $ nextflow run nf-core/chipseq -profile test,singularity...
### Description of the bug Error running the pipeline self-test with conda. ### Command used and terminal output ```console $ nextflow run nf-core/chipseq -profile test,conda --outdir . ... Execution cancelled...