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The confirmation of protocol #83

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NJU-Bio-Info opened this issue Nov 5, 2021 · 1 comment
Open

The confirmation of protocol #83

NJU-Bio-Info opened this issue Nov 5, 2021 · 1 comment

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@NJU-Bio-Info
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Hello, when I use peppro, I have set the protocol as GROSEQ in csv file but when I run looper run .yaml, it tells me that the protocol passed to peppro is pro. How can I solve this problem? Thank you

@NJU-Bio-Info
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This is my csv file:
sample_name,organism,protocol,read_type,read1
Hela_1,human,GROSEQ,single,R1
Hela_2,human,GROSEQ,single,R1

And this is the message after I submit the task, it tells me the protocol is PRO:

Arguments passed to pipeline:

  •       `TSS_name`:  `None`
    
  •        `adapter`:  `cutadapt`
    
  •      `anno_name`:  `None`
    
  •     `complexity`:  `False`
    
  •    `config_file`:  `peppro.yaml`
    
  •          `cores`:  `12`
    
  •       `coverage`:  `False`
    
  •          `dedup`:  `seqkit`
    
  •          `dirty`:  `False`
    
  • ensembl_gene_body: None
  •    `ensembl_tss`:  `None`
    
  •      `exon_name`:  `None`
    
  •   `force_follow`:  `False`
    
  • genome_assembly: hg38
  •          `input`:  `['/share/home/ShuiKM/peppro_tutorial/tools//peppro/examples/data/Hela_2_r1.fq.gz']`
    
  •         `input2`:  `None`
    
  •    `intron_name`:  `None`
    
  •           `keep`:  `False`
    
  •         `logdev`:  `False`
    
  •        `max_len`:  `-1`
    
  •            `mem`:  `12000`
    
  •      `new_start`:  `False`
    
  •        `no_fifo`:  `False`
    
  •  `output_parent`:  `/share/home/ShuiKM/GRO_seq/public_data/Hela/peppro_Hela//peppro/peppro_test/results_pipeline`
    
  •     `paired_end`:  `False`
    
  •       `pre_name`:  `None`
    
  •  `prealignments`:  `[]`
    
  •     `prioritize`:  `False`
    

*** protocol: pro**

  •        `recover`:  `False`
    
  •    `sample_name`:  `Hela_2`
    
  •          `scale`:  `False`
    
  •    `search_file`:  `None`
    
  •         `silent`:  `False`
    
  • single_or_paired: single
  •            `sob`:  `False`
    
  •       `testmode`:  `False`
    
  •        `trimmer`:  `seqtk`
    
  •        `umi_len`:  `0`
    
  •      `verbosity`:  `None`
    

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