Error in the collapse process

[fedeago]

Hi, thanks for your work. I'm tring to run this pipeline but it stop with the following error.

Error executing process > 'bowtie_miRBase_hairpin_collapsed (10.umitransformed.clean.fastq 10.umitransformed.clean_trimmed_umi_trimmed.fastq)

Caused by:
  No such property: baseName for class: nextflow.util.BlankSeparatedList

Source block:
  index_base = index.toString().tokenize(' ')[0].tokenize('.')[0]
  prefix = reads.baseName
  seq_center = params.seq_center ? "--sam-RG ID:${prefix} --sam-RG 'CN:${params.seq_center}'" : ''
  """
      bowtie \\
          $index_base \\
          -p ${task.cpus} \\
          -t \\
          -k 50 \\
          -a \\
          --best \\
          --strata \\
          -e 99999 \\
          --chunkmbs 2048 \\
          -q <(cat $reads) \\
          -S $seq_center \\
          | samtools view -bS - > ${prefix}.bam
      """

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

i use that pipeline with this configuration:

~/nextflow run nf-core/smrnaseq --reads '../cleaned/*.umitransformed.clean.fq.gz' --min_length 17 --genome 'GRCh37' --skipQC -profile singularity

How could i resolve this problem?

[ewels]

Hi @fedeago,

What version of Nextflow are you using? Could you please post the .nextflow.log file from the run?

Phil

[fedeago]

I have't the .nexflow.log file. I use it with slurm, and the reads that i use are already trimmed. I can post the slurm.out file with the standard output of the pipeline. The version of nextflow is 19.10.0.

[ewels]

It looks like the problem is the prefix = reads.baseName bit. I guess it works when there is only one file in the collapsed_fasta channel, but it's breaking here because there is more than one fastq being generated by the seqcluster collapse process for some reason.

@lpantano could you have a look at this please? Am I right?

Phil

[fedeago]

It is a big file, if you like i can post it as text.
slurm.txt

[lpantano]

@ewels you are right, it is detecting UMIs and creating two files, I will work on the fix on Monday.

[apeltzer]

Looks like this is long resolved by @lpantano 👍🏻