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FloWuenne avatar FloWuenne commented on September 25, 2024

This issue is discussing the same problems as described by these two for nf-core/rnaseq:

nf-core/rnaseq#1140
nf-core/rnaseq#1100

from viralrecon.

FloWuenne avatar FloWuenne commented on September 25, 2024

Apologies, I forgot to put the error message from Nextflow that is returned when trying to run with the outdated version of fastqc.

To reproduce, one can run nf-core/viralrecon profile": "test_full" and fusion and wave enabled. This will result in the following error:

Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (SAMPLE_35)'

Caused by:
  Task failed to start - CannotPullContainerError: image verification failed for digest sha256:92c044ab3d3ca1a450f2d0615019ef48db79637249f5fb2ebef256ecaf764541

Command executed:

  printf "%s %s\n" GOL2051A67504_S137_L002_R1_001.fastq.gz SAMPLE_35_1.gz GOL2051A67504_S137_L002_R2_001.fastq.gz SAMPLE_35_2.gz | while read old_name new_name; do
      [ -f "${new_name}" ] || ln -s $old_name $new_name
  done
  fastqc --quiet --threads 6 SAMPLE_35_1.gz SAMPLE_35_2.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VIRALRECON:ILLUMINA:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW":
      fastqc: $( fastqc --version | sed -e "s/FastQC v//g" )
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

from viralrecon.

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