Validate `--max_memory` and `--max_time` parameters and exit if not a valid Nextflow resource unit

[ge2sasag]

Hi,

I got the following error when using the UMI arguments:

Pipeline completed with errors-
Error executing process > 'RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (COMBI_R1)'

Caused by:
  Process `RNASEQ:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (COMBI_R1)` terminated with an error exit status (1)

Command executed:

  umi_tools \
      extract \
      -I COMBI_R1_1.merged.fastq.gz \
      --read2-in=COMBI_R1_2.merged.fastq.gz \
      -S COMBI_R1.umi_extract_1.fastq.gz \
      --read2-out=COMBI_R1.umi_extract_2.fastq.gz \
      null --extract-method=string --bc-pattern='NNNNNNNNNN' \
      > COMBI_R1.umi_extract.log
  
  umi_tools --version | sed -e "s/UMI-tools version: //g" > umitools.version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  Traceback (most recent call last):
    File "/usr/local/bin/umi_tools", line 11, in <module>
      sys.exit(main())
    File "/usr/local/lib/python3.7/site-packages/umi_tools/umi_tools.py", line 61, in main
      module.main(sys.argv)
    File "/usr/local/lib/python3.7/site-packages/umi_tools/extract.py", line 397, in main
      read1s, read2s, strict):
    File "/usr/local/lib/python3.7/site-packages/umi_tools/umi_methods.py", line 123, in joinedFastqIterate
      (pair_id, read2.identifier.split()[0]))
  ValueError: 
  Read pairs do not match
  V300079372L2C001R00100005413/1 != V300079372L2C001R00100005413/2

Work dir:
  /media/gema/GNOMICS/Exp_001_20201029_Barraondo_CIMA/work/e6/998066cf9ce32d2d6fe17d9c917bb5

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

@drpatelh suggested that this is because there is an space between the read name and the info containing /1 or /2 but the read names in my fastq files don't have such space (https://nfcore.slack.com/archives/CE8SSJV3N/p1605808087159800)

My command:

nextflow run nf-core/rnaseq -profile docker -r 2.0 --input ./samplesheet_cut.csv --genome GRCm38 --max_memory '42 GB' --max_time '72.h' --outdir results --skip_fastqc --save_unaligned --save_reference  --with_umi --save_umi_intermeds --umitools_bc_pattern 'NNNNNNNNNN'

nf-core/rnaseq v2.0
nextflow version 20.10.0.5430

[apeltzer]

Moved this to nf-core/rnaseq instead of tools ;-)

[drpatelh]

Ah, sorry, the actual issue I wanted to highlight on tools was that using --max_memory 80 should be validated properly as a Nextflow memory unit and if not to generate an error. The correct way of specifying this would be for example --max_memory '42 GB' otherwise the pipeline just allocates a memory value of 0 and still proceeds as normal.

[ge2sasag]

Oh ok! I thought you meant the umi error sorry!

[drpatelh]

Created a new issue for this nf-core/tools#793