Error in picard markduplicates step

[nilesh-tawari]

Hi @apeltzer,

Thanks for the wonderful pipeline. I am trying to use pipeline for mordern DNA analysis. While running I encountered error in picard markduplicates step:

Below is the command used to run pipeline,

nextflow run nf-core/eager  --pairedEnd --reads '*_R{1,2}_001.fastq.gz' -c ~/.nextflow/config-eager --fasta genome.fa --saveReference --skip_damage_calculation --bwamem --dedupper markdup

Below is the snippet from error.

Command executed:

  picard MarkDuplicates INPUT=sample.sorted.bam.filtered.bam OUTPUT=sample.sorted.bam.filtered.markDup.bam REMOVE_DUPLICATES=TRUE AS=TRUE METRICS_FILE=sample.sorted.bam.filtered.markdup.metrics" VALIDATION_STRINGENCY=SILENT

Command exit status:
  2

Command output:
  (empty)

Command error:
  .command.sh: line 2: unexpected EOF while looking for matching `"'

There is formetting error in .commands.sh file

Thank you

[apeltzer]

Hi @nilesh-tawari !
Please use the -r dev branch for now, I included a fix for your problem that should resolve the missing " in 018a522 !

I'll close the issue, please re-open if the problem persists after this!

[nilesh-tawari]

@apeltzer, Thanks yes the issue is solved. One more minor bug, the pigz dependency is missing in conda environment file. Hence, pipeline fails.

[apeltzer]

Hm, its not in the dev branch, but the stable pipeline release uses something else. I'll probably fix the 1-2 remaining issues today and release a new minor release to fix all of these.