Print nuclear contamination fails (input files not staged)

[IdoBar]

Check Documentation

I have checked the following places for your error:

• nf-core website: troubleshooting
• nf-core/eager pipeline documentation
  - nf-core/eager FAQ/troubleshooting can be found here

Description of the bug

Print nuclear contamination process fails because input files not staged properly (or their folder not bound to singularity) and are not available for print_x_contamination.py

Steps to reproduce

Steps to reproduce the behaviour:

1. Command line: nextflow run nf-core/eager -r 2.3.1 -params-file $BATCH.$REF.$ALIGNER.$GENOTYPER.json -c $HOME/.nextflow/qris.config --run_nuclear_contamination true
2. See error below

Expected behaviour

Process print_nuclear_contamination should complete successfully.

Log files

Have you provided the following extra information/files:

• The command used to run the pipeline

• The .nextflow.log file

• The exact error:

Error executing process > 'print_nuclear_contamination'

Caused by:
  Process `print_nuclear_contamination` terminated with an error exit status (1)

Command executed:

  print_x_contamination.py /gpfs1/scratch/30days/ibar/data/Human/WWR/WWR_NF1_process_14_01_2021/work/66/55a91e9b518c14871a04bde5f4c3ea/UWW1_T.X.contamination.out /gpfs1/scratch/30days/ibar/data/Human/WWR/WWR_NF1_process_14_01_2021/work/65/b35ed87179673efedd082c3e5253b5/UWW1_BP.X.contamination.out /gpfs1/scratch/30days/ibar/data/Human/WWR/WWR_NF1_process_14_01_2021/work/78/de48ec85aa16c1b8b26ff23d203cd5/UWW1_B.X.contamination.out

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/ibar/.nextflow/assets/nf-core/eager/bin/print_x_contamination.py", line 40, in <module>
      with open(fn, 'r') as f:
  FileNotFoundError: [Errno 2] No such file or directory: '/gpfs1/scratch/30days/ibar/data/Human/WWR/WWR_NF1_process_14_01_2021/work/66/55a91e9b518c14871a04bde5f4c3ea/UWW1_T.X.contamination.out'

Work dir:
  /gpfs1/scratch/30days/ibar/data/Human/WWR/WWR_NF1_process_14_01_2021/work/ee/8e69d3c9294f243ad37369370b0c27

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out

System

• Hardware: HPC
• Executor: PBSPro
• OS: RHEL
• Version Linux 3.10.0-693.5.2.el7.x86_64
• Runtime: Groovy 3.0.5 on OpenJDK 64-Bit Server VM 11.0.1+13-LTS

Nextflow Installation

• Version: 20.10.0 build 5430

Container engine

• Engine: Singularity
• version: 3.6.3
• Image tag: nfcore/eager:2.3.1

Additional context

I'm not exactly sure how nextflow stages input files, but my guess is that because the input files for the print_nuclear_contamination process is provided with val 'Contam' from ch_from_nuclear_contamination.map { it[7] }.collect() instead of as path, then the files were not staged properly, see below the content of the stage process in .command.run:

nxf_stage() {
    true
}

I could get the command to run successfully when I bind the work folders of each sample's nuclear_contamination run to singularity with -B flag.

[apeltzer]

That does sound a bit odd tbh, pinging @TCLamnidis on that one as he's the expert on the contamination step.

[IdoBar]

@apeltzer, I believe that this is a nextflow scripting issue than the actual nuclear contamination command itself.

[jfy133]

@IdoBar 's comments in slack could indeed be relevant. Could either be an issue with angsd not making any output, or that the processes using a val to specify input stuff (this has been a problem in the past too).

[IdoBar]

I just tested it and it's an easy fix, just replace the val with path and it works.

[jfy133]

Ok that's promising, but need to verify with @TCLamnidis iirc there was a problem with that originally...