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nf-core / circrna

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
https://nf-co.re/circrna
MIT License
45 stars 24 forks source link

ERROR ~ Argument of `file` function cannot be null #127

Closed ZabalaAitor closed 5 months ago

ZabalaAitor commented 5 months ago

Description of the bug

I cannot run nf-core/circRNA. The code works on other computers and in a cluster.

Command used and terminal output

nextflow run nf-core/circRNA 
          -r dev -profile apptainer 
          --input data/samplesheet_circRNA.csv 
          --module circrna_discovery 
          --outdir /home/neuroim/Desktop/results_circRNA 
          --tool 'ciriquant','circexplorer2','find_circ','circrna_finder','dcc','segemehl' 
          --max_cpus 12 
          --max_memory 64GB 
          -w /home/neuroim/Desktop/work_rnaseq 
          --genome GRCh38 
          --save_reference false 
          --bowtie /data/index/bowtie/ 
          --bowtie2 /data/index/bowtie2/ 
          --bwa /data/index/bwa/ 
          --star /data/index/star/ 
          --segemehl /data/index/segemehl/ 
          --hisat2 /data/index/hisat2/ 
          --skip_fastqc

 N E X T F L O W   ~  version 24.04.2

NOTE: Your local project version looks outdated - a different revision is available in the remote repository [d5967c5273]
Launching `https://github.com/nf-core/circRNA` [intergalactic_ampere] DSL2 - revision: 5ddc061929 [dev]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/circrna vdev-g5ddc061
------------------------------------------------------
Core Nextflow options
  revision       : dev
  runName        : intergalactic_ampere
  containerEngine: apptainer
  launchDir      : /data/RNAseq_MS
  workDir        : /home/neuroim/Desktop/work_rnaseq
  projectDir     : /home/neuroim/.nextflow/assets/nf-core/circRNA
  userName       : neuroim
  profile        : apptainer
  configFiles    : 

Input/output options
  input          : data/samplesheet_circRNA.csv
  outdir         : /home/neuroim/Desktop/results_circRNA

Pipeline Options
  tool           : ciriquant,circexplorer2,find_circ,circrna_finder,dcc,segemehl

Reference genome options
  save_reference : false
  genome         : GRCh38
  fasta          : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa
  gtf            : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf
  mature         : s3://ngi-igenomes/igenomes//Homo_sapiens/NCBI/GRCh38/Annotation/SmallRNA/mature.fa
  bowtie         : /data/index/bowtie/
  bowtie2        : /data/index/bowtie2/
  bwa            : /data/index/bwa/
  hisat2         : /data/index/hisat2/
  segemehl       : /data/index/segemehl/
  star           : /data/index/star/

Read trimming options
  skip_fastqc    : true

Max job request options
  max_cpus       : 12
  max_memory     : 64GB

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

* The pipeline

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

* Software dependencies
  https://github.com/nf-core/circrna/blob/master/CITATIONS.md
------------------------------------------------------
ERROR ~ Argument of `file` function cannot be null

 -- Check script '/home/neuroim/.nextflow/assets/nf-core/circRNA/main.nf' at line: 62 or see '.nextflow.log' file for more details

Relevant files

No response

System information

Nextflow: 24.04.2.5914 Hardware: Desktop Executor: local Conatiner: Docker, Singularity, Apptainer, Conda OS: Linux nf-core/circrna: dev

nictru commented 5 months ago

Hey, you are missing the phenotype parameter. I know this is not marked required in the documentation and a fix is already on the way. For now you should just provide a dummy table to make it work

Also you should probably update the pipeline, your version is 3 weeks old.

ZabalaAitor commented 5 months ago

Hey, Thank you very much for your quick response. A newbie question: how can I update the pipeline?

nictru commented 5 months ago

This should do it (docs): nextflow pull nf-core/circrna

ZabalaAitor commented 5 months ago

Thank you so much!

nictru commented 5 months ago

No problem! Feel free to close the issues once you have a working run :)