nf-core/sammyseq

Issues

• Still present the warning on old parameter name "bwa_index" and maybe not using the index provided with --bwa

  #26 opened a year ago by daisymut
  0

• URGENT: pin nf-validation version

  #29 opened a month ago by nvnieuwk
  1

• Update modules having a new version available

  #22 opened a year ago by daisymut
  0

• Rename parameters to comply with igenomes configuration

  #20 opened a year ago by daisymut
  0

• Add fastqc after trimming

  #16 opened a year ago by daisymut
  0

• Markduplicates should mark and not remove duplicate reads

  #17 opened a year ago by daisymut
  0

• Broken links in multiqc report

  #19 opened a year ago by daisymut
  0

• Reorder output folder structure

  #13 opened a year ago by daisymut
  0

• Multiqc should be launched at the end and collect stats and outputs from all preceding steps

  #8 opened a year ago by daisymut
  0

• Use bwa_index as the starting point instead of the 'fasta only' option

  #9 opened a year ago by lucidif
  0

• Sample name should not be changed and fastq produced from the same sample should be cat together

  #11 opened a year ago by daisymut
  0

• Cat fastq should be optional

  #10 opened a year ago by daisymut
  0

• Make smaller test data Single End

  #7 opened a year ago by daisymut
  1

• Change reference in test profile to the already available human chr20_hg38

  #12 opened a year ago by daisymut
  1