#C05785S3TMX Hi, I thank you for your efforts in developing riboseq pipeline. This is my first time to use nf-core 🙂. I have a question in "with_umi" option. When I turn on "with_umi" option, the run is failed with below message (If I do not use "with_umi", then it works well). It would be grateful if somebody helps me..!

Core Nextflow options
  revision              : 1.0.1
  runName               : shrivelled_mahavira
  containerEngine       : docker
  launchDir             : /data/chois/riboseq/nf_riboseq
  workDir               : /data/chois/riboseq/nf_riboseq/work
  projectDir            : /home/chois/.nextflow/assets/nf-core/riboseq
  userName              : chois
  profile               : docker
  configFiles           :

Input/output options
  input                 : samplesheet_HBL1_D.csv
  outdir                : output_HBL1_D

Reference genome options
  fasta                 : <s3://references_gencode42_hg38/genome.fa>
  gtf                   : <s3://references_gencode42_hg38/annotation.gtf>
  transcript_fasta      : <s3://references_gencode42_hg38/transcript.fa>

UMI options
  with_umi              : true
  umitools_bc_pattern   : NNNNNN
  umitools_umi_separator: _

Alignment options
  min_mapped_reads      : 5

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/riboseq for your analysis please cite:

* The pipeline
  <https://doi.org/10.5281/zenodo.10966364>

* The nf-core framework
  <https://doi.org/10.1038/s41587-020-0439-x>

* Software dependencies
  <https://github.com/nf-core/riboseq/blob/master/CITATIONS.md>
------------------------------------------------------
WARN: Access to undefined parameter `pseudo_aligner` -- Initialise it to a default value eg. `params.pseudo_aligner = some_value`
[-        ] process > NFCORE_RIBOSEQ:PREPARE_GENOME:GTF_FILTER                                                                           -
[-        ] process > NFCORE_RIBOSEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES                                                                 -
[-        ] process > NFCORE_RIBOSEQ:PREPARE_GENOME:SORTMERNA_INDEX                                                                      -
[-        ] process > NFCORE_RIBOSEQ:PREPARE_GENOME:STAR_GENOMEGENERATE                                                                  -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:CAT_FASTQ                                                                 -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC                                   -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT                         -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE                               -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:SORTMERNA                                                                 -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX                                    -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE                                    -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:PREPROCESS_RNASEQ:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT                                    -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:STAR_ALIGN                                                                 -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_SORT                               -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:SAMTOOLS_INDEX                              -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS           -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT        -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS        -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_SORT                        -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:SAMTOOLS_INDEX                       -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS    -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT -
[-        ] process > NFCORE_RIBOSEQ:RIBOSEQ:FASTQ_ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS_TRANSCRIPTOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS -
WARN: Access to undefined parameter `salmon_index` -- Initialise it to a default value eg. `params.salmon_index = some_value`
WARN: Access to undefined parameter `sortmerna_index` -- Initialise it to a default value eg. `params.sortmerna_index = some_value`
Missing process or function BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME()

 -- Check script '/home/chois/.nextflow/assets/nf-core/riboseq/main.nf' at line: 102 or see '.nextflow.log' file for more details

Looks like a bug, thanks, could you create an issue? https://github.com/nf-core/riboseq/issues

Thanks for your quick reply! I posted the issue on the github. 🙂