nf-core/chipseq

Issues

• Process `NFCORE_CHIPSEQ:PREPARE_GENOME:GFFREAD` declares 2 input channels but 1 were specified

  #432 opened a month ago by ftabaro
  0

• nextflow.script.ScriptBinding.check_max()

  #335 opened 5 months ago by fgualdr
  3

• Process `NFCORE_CHIPSEQ:CHIPSEQ:FASTQ_ALIGN_BWA:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (SRR5627136_REP2_T1)` terminated with an error exit status (1)

  #431 opened 2 months ago by NicoleChant
  0

• Not a valid path value when provide genome by fasta and gtf in compressed gz format, and not providing genome index or gene bed

  #427 opened 2 months ago by ljw20180420
  1

• cutadapt `trim_nextseq` config typo

  #429 opened 2 months ago by cmatKhan
  1

• Process `NFCORE_CHIPSEQ:CHIPSEQ:MULTIQC` terminated with an error exit status

  #428 opened 2 months ago by Sungryong-Oh
  0

• Can't run if there is no control

  #384 opened 5 months ago by d-jch
  3

• Refactor local modules to use an conda environment yml file and not ping modules directly

  #417 opened 3 months ago by JoseEspinosa
  0

• Move the KHMER_UNIQUEKMERS logic to prepare_genome

  #416 opened 3 months ago by JoseEspinosa
  0

• Permission denied at the beginning of the pipeline

  #414 opened 3 months ago by paolamaragno
  0

• Error: Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BOWTIE2:BOWTIE2_ALIGN (WT_HA_IP_REP1_T1)` terminated with an error exit status (1)

  #411 opened 4 months ago by Sungryong-Oh
  1

• Update modules and subworkflows for 2.1.0 release

  #409 opened 5 months ago by JoseEspinosa
  2

• MACS2 steps did not carried out

  #336 opened 5 months ago by wook2014
  4

• Normalisation of bigwig files

  #357 opened 5 months ago by alhh507
  5

• Default values for p-value and FDR

  #364 opened 5 months ago by amibe1
  2

• MACS2: Too few paired peaks (0) so I can not build the model!

  #374 opened 5 months ago by dannyjwan
  2

• Error running the pipline test in the BWA index step

  #376 opened 5 months ago by Alhajuji
  2

• Macs2 Output

  #388 opened 5 months ago by kittyBS
  2

• Error converting BAM to tagalign file

  #316 opened 5 months ago by CLAIRE-cuhk
  4

• Spike ins normalization

  #321 opened 2 years ago by EmanuelSoda
  12

• Add --only_step options

  #337 opened 2 years ago by IStevant
  0

• Error with NextSeq trimming

  #375 opened 5 months ago by gitMakeCoffee
  2

• Get rid of checksamplesheet.py and switch to nf-schema

  #403 opened 5 months ago by JoseEspinosa
  0

• IDR analysis

  #386 opened 5 months ago by ZeinBader
  2

• nf-core download skips 'bowtie2 align' singularity image with container string parsing error

  #318 opened 5 months ago by rdwngs
  4

• Both '--read_length' and '--macs_gsize' not specified! Please specify either to infer MACS2 genome size for peak calling.

  #328 opened 5 months ago by ariadnaaterrades
  2

• Samplesheet description in the documentation

  #320 opened 5 months ago by IStevant
  3

• Error exit status (1) in NFCORE_CHIPSEQ:CHIPSEQ:CUSTOM_DUMPSOFTWAREVERSIONS

  #333 opened 5 months ago by nayem-haque
  3

• Provide replicate information explicitly in samplesheet

  #343 opened 5 months ago by JoseEspinosa
  6

• chipseq - samplesheet doesn't have minimum number of columns

  #319 opened 5 months ago by BalajiVenkadakrishnan
  2

• Header missing is in bowtie2 outputted bam files

  #347 opened 5 months ago by chiefcat
  1

• package or namespace load failed for ‘UpSetR’

  #360 opened 5 months ago by Nicobouch
  4

• minor "samplesheet_pe.csv" format issue

  #369 opened 5 months ago by hukai916
  1

• Update MACS to v3

  #378 opened 5 months ago by alexpmagalhaes
  1

• Get rid of checkIfExists for params paths

  #367 opened 5 months ago by JoseEspinosa
  1

• The "sample" field from the samplesheet is too lenient

  #396 opened 5 months ago by JoseEspinosa
  1

• Streamline nf-core/chipseq and nf-core/atacseq by using shared subworkflows

  #398 opened 6 months ago by bjlang
  0

• Improve website on parameters section Alignment Options for argument --save_unaligned

  #385 opened 6 months ago by aghr
  1

• Remove lib folder to get ready for v2.13.1 template merge

  #387 opened 6 months ago by JoseEspinosa
  1

• There are multiple files for each of the following file names

  #382 opened 10 months ago by smsobera
  0

• jobs failing with sigbus and unknown userid errors

  #377 opened a year ago by mniederhuber
  1

• No Space left on device error

  #361 opened a year ago by Shashankti
  3

• PHANTOMPEAKQUALTOOLS throws stack overflow exception

  #370 opened a year ago by krokicki
  1

• Make subworkflows & modules available for nf-core tools

  #362 opened a year ago by kelly-sovacool
  1

• Process `NFCORE_CHIPSEQ:CHIPSEQ:ALIGN_BWA_MEM:BWA_MEM (EBAC_Input_REP2_T1)` terminated with an error exit status (1)

  #355 opened a year ago by JiahuaQu
  3

• mergeBed ERROR: Requested column 10, but database file - only has fields 1 - 9.

  #356 opened a year ago by JiahuaQu
  18

• Problem with samplesheet

  #348 opened 2 years ago by peculiar97
  3

• Metro map draft for nf-core/chipseq

  #317 opened 2 years ago by G-Sarah
  1

• nextflow intogen.nf error: No such variable: input

  #334 opened 2 years ago by tanayb001
  1

• Error 404 for ChIP-seq assets/blacklists

  #330 opened 2 years ago by FelixKrueger
  0