nf-core/smrnaseq

Issues

• No Reference genome availabe in miRBase and MirGeneDB

  #487 opened 13 days ago by sajjadasaf
  1

• mirtrace_species variable not defined

  #488 opened 11 days ago by kopichris
  1

• Error executing process > 'NFCORE_SMRNASEQ:MIRNA_QUANT:SEQCLUSTER_COLLAPSE

  #485 opened 13 days ago by sajjadasaf
  3

• CSVTK join too slow for large projects

  #484 opened a month ago by apeltzer
  4

• pipeline fails at same step each time

  #453 opened 21 days ago by lo-schwartz
  4

• Cant run pipeline with newer nextflow version

  #480 opened a month ago by nschcolnicov
  1

• MIRTOP_STATS IndexError

  #477 opened a month ago by anastasiaprime
  4

• Change to `=` assignment, see above

  #470 opened 3 months ago by apeltzer
  0

• Fix linting

  #458 opened 3 months ago by atrigila
  1

• Review pipeline release checklist

  #460 opened 3 months ago by atrigila
  5

• Add licences to bin scripts

  #465 opened 3 months ago by apeltzer
  0

• Validate parameters centrally via utility functions

  #467 opened 2 months ago by apeltzer
  0

• Make citation tools dependent on whether tool was executed

  #468 opened 2 months ago by apeltzer
  1

• Add nf-core `mirdeep` to smrnaseq

  #443 opened 3 months ago by atrigila
  0

• Add nf-core `bowtie align` to smrnaseq

  #436 opened 3 months ago by atrigila
  1

• Update `mirtop` to latest version

  #437 opened 3 months ago by atrigila
  0

• Upgrade Modules - and include Umicollapse into MQC report

  #428 opened 3 months ago by apeltzer
  2

• Create nf-core `mirdeep` module

  #431 opened 3 months ago by atrigila
  0

• Raise minimum NXF version

  #424 opened 3 months ago by apeltzer
  0

• Add nf-core `bowtie1 build` to smrnaseq

  #433 opened 3 months ago by atrigila
  0

• Add nf-core `bowtie2 build` to smrnaseq

  #434 opened 3 months ago by atrigila
  0

• The pipeline doesn't finish but is marked as completed

  #415 opened 3 months ago by karlaarz
  13

• Add nf-core `seqcluster` to smrnaseq

  #416 opened 3 months ago by atrigila
  1

• Add nf-core `mirtop` module to smrnaseq

  #417 opened 3 months ago by atrigila
  1

• Error in 'NFCORE_SMRNASEQ:MIRTRACE' for paired data

  #421 opened 3 months ago by ranxm2
  9

• Replace custom code with nf-core/modules/pigz/uncompress

  #422 opened 3 months ago by apeltzer
  1

• Pipeline should warn / crash for users with warning upon supply of PE data

  #423 opened 3 months ago by apeltzer
  0

• Create nf-core `mirTrace` module

  #402 opened 4 months ago by atrigila
  0

• Migrate local `BLAT` to nf-core modules

  #395 opened 4 months ago by atrigila
  0

• Create nf-core `mirtop` module

  #403 opened 4 months ago by atrigila
  0

• Umicollapse algo wrong set

  #404 opened 4 months ago by apeltzer
  0

• Improve the contaminant filter

  #406 opened 3 months ago by apeltzer
  2

• Fix Nextflex 4nt 3p trimming

  #407 opened 4 months ago by lpantano
  3

• Paired-end data?

  #475 opened 2 months ago by anastasiaprime
  4

• Reorganize `CLEAN_FASTA` function

  #455 opened 3 months ago by atrigila
  1

• edger_qc module nf-test is trying to check for undeterministic files and it fails

  #450 opened 3 months ago by nschcolnicov
  2

• Addressing TODOs in pipeline, general cleanup of variables

  #400 opened 3 months ago by nschcolnicov
  2

• Replace untarfiles with untar

  #449 opened 3 months ago by nschcolnicov
  1

• standardize ch_bowtie_index channel structure

  #451 opened 3 months ago by nschcolnicov
  0

• Generate test profile for mirdeep subworkflow

  #399 opened 3 months ago by nschcolnicov
  0

• Possible bug in logic code related to mature, hairpin and species setup

  #414 opened 3 months ago by lpantano
  4

• Analysis of Paired-end reads

  #440 opened 3 months ago by oliverdesousa
  1

• Assess which files should be published

  #393 opened 3 months ago by nschcolnicov
  4

• Assess converting local modules to nf-core

  #392 opened 3 months ago by nschcolnicov
  1

• Add nf-core `mirTrace` module to smrnaseq

  #410 opened 3 months ago by atrigila
  0

• mirTrace produces an error in test nextflex

  #419 opened 3 months ago by atrigila
  2

• Create nf-core `seqcluster` module

  #413 opened 3 months ago by atrigila
  0

• genome-wide smrna detection and quantification

  #409 opened 4 months ago by lpantano
  2

• Create nf-core `mirTrace` module

  #401 opened 4 months ago by atrigila
  1

• Pipeline not using channels for all inputs

  #390 opened 4 months ago by nschcolnicov
  1