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nf-core / cutandrun

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
https://nf-co.re/cutandrun
MIT License
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Include statement is not allowed within a workflow definition #41

Closed cjfields closed 2 years ago

cjfields commented 3 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

I am seeing Include statement is not allowed within a workflow definition when running cutnrun:

$ nextflow run ../src/cutandrun -c cutnrun.conf -profile uiuc_hpcbio --custom_config_base /home/a-m/cjflds/projects/zhao5/2021-June-CutAndRun/src/configs -resume -qs 3 -with-report -with-trace
N E X T F L O W  ~  version 21.06.0-edge
Launching `../src/cutandrun/main.nf` [serene_ride] - revision: 0041d1bad8

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/cutandrun v1.0.0dev
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Core Nextflow options
  runName                   : serene_ride
  containerEngine           : singularity
  launchDir                 : /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/results
  workDir                   : /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/results/work
  projectDir                : /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/src/cutandrun
  userName                  : cjfields
  profile                   : uiuc_hpcbio
  configFiles               : /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/src/cutandrun/nextflow.config, /home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/results/cutnrun.conf

Input/output options
  input                     : samplesheet.csv
  email                     : cjfields@illinois.edu
  save_reference            : true

Reference data options
  gtf                       : /home/groups/hpcbio/references/nextflow/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf
  blacklist                 : /home/a-m/cjfields/projects/zhao5/2021-June-CutAndRun/data/reference/ENCFF356LFX.bed
  spikein_fasta             : /home/a-m/cjfields/projects/zhao5/2021-June-CutAndRun/data/reference/GCF_000146045.2_R64_genomic.fna
  fasta                     : /home/a-m/cjfields/projects/zhao5/2021-June-CutAndRun/data/reference/GRCh38_flu_RSV.fa
  igenomes_base             : /home/groups/hpcbio/references/nextflow

Pipeline Options
  igg_control               : false
  gene_bed                  : /home/groups/hpcbio/references/nextflow/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed

Institutional config options
  custom_config_base        : /home/a-m/cjfields/projects/zhao5/2021-June-CutAndRun/src/configs
  config_profile_description: University of Illinois IGB Biocluster set up, base provided by nf-core/configs.
  config_profile_contact    : Chris Fields (cjfields - at - illinois.edu)
  config_profile_url        : https://http://biocluster.igb.illinois.edu/

Max job request options
  max_cpus                  : 24
  max_memory                : 500 GB
  max_time                  : 24d 20h 31m 24s

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/cutandrun for your analysis please cite:

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/cutandrun/blob/master/CITATIONS.md
------------------------------------------------------
Include statement is not allowed within a workflow definition

 -- Check script '/home/groups/hpcbio/projects/zhao5/2021-June-CutAndRun/src/cutandrun/main.nf' at line: 64 or see '.nextflow.log' file for more details

Steps to reproduce

Steps to reproduce the behaviour:

  1. Command line: nextflow run cutandrun -c cutnrun.conf -profile uiuc_hpcbio --custom_config_base /home/a-m/cjflds/projects/zhao5/2021-June-CutAndRun/src/configs -resume -qs 3 -with-report -with-trace
  2. See error: Include statement is not allowed within a workflow definition

Expected behaviour

Workflow runs

Log files

Have you provided the following extra information/files:

System

Nextflow Installation

Container engine

cjfields commented 3 years ago

Working on a quick pull request for this, it's an easy fix.

chris-cheshire commented 3 years ago

Thanks for posting / fixing this!

chris-cheshire commented 3 years ago

As a rule - I wouldnt use the edge versions unless you have to, as they may include breaking changes such as the one above.

cjfields commented 2 years ago

Thx @chris-cheshire , closing this out!