Nextflow Practice

Practical activity

• January 15, 2024 (Monday)
• 4pm - 6pm BRT
• Online: Google Meet

PS: if you want to join the meeting, please send an email to @SantosRAC by January 14, 2024 (Sunday).

Contact information:

• Renato Augusto Corrêa dos Santos @SantosRAC

Requirements

• Nextflow version 23.10.0 build 5889
• ffq v0.3
• Trimmomatic v0.39

Pipeline execution

cd nextflow
nextflow run nextflow_pratice.nf -c ../nextflow.config
# if docker requires sudo
sudo /path/to/nextflow nextflow_pratice.nf -c ../nextflow.config

@jomare1188 suggested to add the following parameters to the command line: -with-report -with-dag. They provide a report and a DAG graph, respectively.

sudo /path/to/nextflow nextflow_pratice.nf -c ../nextflow.config -with-report -with-dag --reads "SRR6665476"

--reads "SRR6665476" changes the value of params.reads variable in the nextflow.nf file.

After the activity, we added a report and a DAG graph to the /results folder, providing examples of workflows that failed and succeeded.

Organizers

• Renato Augusto Corrêa dos Santos @SantosRAC
• Pedro Cristovão Carvalho @capuccino26
• Jorge Mario Muñoz Pérez @jomare1188
• Kelly Hidalgo Martinez @khidalgo85
• Beatriz Rodrigues Estevam @Beatriz-Estevam
• Felipe Vaz Peres @felipevzps

References

• Nextflow & nf-core Treinamento Comunitário Online - Sessão 1 (Portuguese) (shared by @khidalgo85)
• Nextflow Official Documentation
• RNA sequencing analysis pipeline (shared by @capuccino26)