nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Kallistobustools subworkflow fails ("no such propery launchDir for class: java.lang.String") #84

Closed apeltzer closed 2 years ago

apeltzer commented 2 years ago

Check Documentation

I have checked the following places for your error:

Description of the bug

Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:KALLISTO_BUSTOOLS:KALLISTOBUSTOOLS_REF (GRCm38.p6.genome.chr19.fa)'

Caused by:
  No such property: launchDir for class: java.lang.String

Source block:
  if (workflow == "standard") {
          """
          kb \\
              ref \\
              -i kb_ref_out.idx \\
              -g t2g.txt \\
              -f1 cdna.fa \\
              --workflow $workflow \\
              $fasta \\
              $gtf

          cat <<-END_VERSIONS > versions.yml
          ${getProcessName(task.process)}:
              ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
          END_VERSIONS
          """
      } else {
          """
          kb \\
              ref \\
              -i kb_ref_out.idx \\
              -g t2g.txt \\
              -f1 cdna.fa \\
              -f2 intron.fa \\
              -c1 cdna_t2c.txt \\
              -c2 intron_t2c.txt \\
              --workflow $workflow \\
              $fasta \\
              $gtf

          cat <<-END_VERSIONS > versions.yml
          ${getProcessName(task.process)}:
              ${getSoftwareName(task.process)}: \$(echo \$(kb --version 2>&1) | sed 's/^.*kb_python //;s/positional arguments.*\$//')
          END_VERSIONS
          """
      }

Work dir:

Steps to reproduce

nextflow run nf-core/scrnaseq -r dev -profile test,<docker/singularity/...>

Expected behaviour

Should not be triggering an error šŸ‘šŸ»

Log files

Have you provided the following extra information/files:

Nextflow Installation

Container engine

@alexblaessle initially found it, reproduced it with the test profile. Might also be that the module for kallistobustools is not function properly šŸ¤”

apeltzer commented 2 years ago

Fixed in #76