Francesco Lescai

Add Rmarkdown module(s) for basic reproducible data analysis

2

Following up on a thread on Slack in #modules, discussing with @drpatelh and @grst: - integration of Rmarkdown with Nextflow - adding Rmarkdown at the end of nf-core pipelines, to...

Add variant calling training material

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This PR adds the training material for variant calling applications, using nf-core/sarek as discussed during the nf-core hackathon in Barcelona 2023. Main features: - a theory recap on variant calling...

This is meant to identify an activity begun at the hackathon-october-2023. The idea is to define a proposal for additional training materials, covering application specific training (such as variant calling...

Update CNVkit

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## PR checklist ### Overall description This PR adds the following improvements to the CNVkit subworkflow(s): - updates the CNVkit modules, as updated in nf-core/modules - with the revised cnvkit/batch...

GCP error in v.3.4.1 "Cloud Storage objects are immutable"

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### Description of the bug Got the error: ``` Apr-24 16:07:17.072 [Actor Thread 40] ERROR nextflow.extension.OperatorImpl - @unknown com.google.cloud.storage.contrib.nio.CloudStorageObjectImmutableException: Cloud Storage objects are immutable. at com.google.cloud.storage.contrib.nio.CloudStorageFileAttributeView.setTimes(CloudStorageFileAttributeView.java:65) at java.base/java.nio.file.CopyMoveHelper.copyToForeignTarget(CopyMoveHelper.java:135) at java.base/java.nio.file.CopyMoveHelper.moveToForeignTarget(CopyMoveHelper.java:157)...