Jose Espinosa-Carrasco
Jose Espinosa-Carrasco
* Move `ANNOTATE_BOOLEAN_PEAKS` under `skip_peak_annotation` in modules.config * Update parameters table in changelog
The test for chromap are failing with the exception below: ```bash Caused by: Process `NFCORE_CHIPSEQ:CHIPSEQ:MACS2_CALLPEAK (SPT5_T0_REP1)` terminated with an error exit status (1) Command executed: macs2 \ callpeak \ --keep-dup...
As mentioned above, the `--preset chip` argument of `chromap` includes the removal of duplicates (`--remove-pcr-duplicates` set by the preset) and thus, the downstream `PRESEQ_LCEXTRAP` process fails with the following error:...
This feature will be needed to implement the IDR logic that need information about the replicates to calculate the reproducibility of the peaks, see #87
### Description of feature From Nextflow version 22.4.0, the DSL2 declaration is not needed anymore at the top of 4.0 script (i.e. `nextflow.enable.dsl = 2`). See [here](https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html). Hence, it can...
The modules that are updated on pipeline release are currently manually listed on the `CHANGELOG.md` see [here](https://github.com/nf-core/rnaseq/blob/master/CHANGELOG.md#software-dependencies). As discussed on [this](https://github.com/nf-core/rnaseq/pull/672) PR, it might be nice to implement an automatic...
From Nextflow version `22.4.0`, the DSL2 declaration is not needed anymore at the top of the script (i.e. `nextflow.enable.dsl = 2`). See [here](https://www.nextflow.io/blog/2022/evolution-of-nextflow-runtime.html). Hence, it can be removed from all...
The input file [here](https://raw.githubusercontent.com/nf-core/test-datasets/atacseq/design.csv) is deprecated update to something similar to [this](https://github.com/nf-core/atacseq/blob/dev/assets/test.csv).
I run a pipeline using nextflow-tower and it worked. Then, I run the same pipeline with a different parameterization from nextflow tower but now I am getting this error. However,...