Error executing process > 'fastqc

[grace-yun-liu]

Hi! I can't tell if there are any previous reports of this error, because I can't seem to see any other issues on the Github.

I recently ran a screen with the Zuber lab's 2-guide human library, using staggered barcodes. Using Nextflow version 22.10.0, I was able to get the test to run with no problems, but I keep running into an error when I input my own data and barcodes.

Because I'm using staggered barcodes, I'm running the version of the pipeline under the fandersch_dev_staggered branch.

PROFILE=${1:-singularity}
echo "Using profile ${PROFILE}."

NXF_VER=22.10.0 nextflow run ZuberLab/crispr-process-nf \
    -r fandersch_dev_staggered \
    -c process_sgRNAs.config \
    -profile ${PROFILE} \
    --library zuber_top2human_library_genomewide.txt \
    --barcodes my_barcodes.txt \
    --inputDir Sequencing/00_fastq \
    --outputDir nextflow_output

Shortly after (successfully, I think) de-multiplexing my samples, I'm thrown the following error:

Error executing process > 'fastqc (Grace1-Grace2-Grace3_R1_001)'

Caused by:
  No such variable: i -- Check script '/root/.nextflow/assets/ZuberLab/crispr-process-nf/main.nf' at line: 404

Source block:
  """
      fastqc -t ${task.cpus} -q ${fastq}
      for i in *_fastqc*; do mv "$i" ${lane}_"$i"; done
      """

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

Would you be able to help me figure out how to solve this issue? I assume that fastqc is getting called by trim_barcode_and_spacer and that it's not finding something in the designated spot, but I'm not sure what the problem might be.

[grace-yun-liu]

I managed to get the process to run by reverting to a prior version of the code, cutting out the following line:
for i in *_fastqc*; do mv "$i" ${lane}_"$i"; done

[fandersch]

Hi,

you are right, there was an issue with my last commit. I fixed this now in the the newest commit.

Could you please check if it works for you now? If you are running it with nextflow run zuberlab/crispr-process-nf, remember to call nextflow pull zuberlab/crispr-process-nf to update the cached pipeline.

[grace-yun-liu]

Hi Florian! The new commit looks great and executed with no problems.