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# hic
  • p
    Your ping didn't work there, but for this pipeline it's mostly @nservant behind the wheel.
  • e
    Would there be interest in starting a hic maintainers team? I think we've seen a lot of success in #CL88J906S and #CP3RJSMF0 adding a crew.
    p
    • 2
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  • a
    hi! just wondering how the bowtie index path is specified. I tried: "bwt2_index": "/zfshomes\/aparikh02\/SetupControls\/Genomes\/mouse_m34\/bowtie\/GRCm39" in my params. and that is the correct path. and the bt indices I downloaded are GRCm39.1.bt2 GRCm39.3.bt2 GRCm39.rev.1.bt2 GRCm39.2.bt2 GRCm39.4.bt2 GRCm39.rev.2.bt2. did I do something wrong?
    n
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    • 2
  • a
    Copy code
    Missing output file(s) `*.html` expected by process `NFCORE_HIC:HIC:FASTQC (prog_iPAX7_Dox_rep3)`

Command executed:

  printf "%s %s\n" prog_iPAX7_Dox_rep3_R1.fastq.gz prog_iPAX7_Dox_rep3_1.gz prog_iPAX7_Dox_rep3_R2.fastq.gz prog_iPAX7_Dox_rep3_2.gz | while read old_name new_name; do
      [ -f "${new_name}" ] || ln -s $old_name $new_name
  done
  fastqc  --threads 6 prog_iPAX7_Dox_rep3_1.gz prog_iPAX7_Dox_rep3_2.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:FASTQC":
      fastqc: $( fastqc --version | sed -e "s/FastQC v//g" )
  END_VERSIONS

Command exit status:
  0

Command output:
  (empty)

Command error:
  WARNING: Skipping mount /opt/ohpc/pub/libs/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
  Started analysis of prog_iPAX7_Dox_rep3_1.gz
  Started analysis of prog_iPAX7_Dox_rep3_2.gz
  Approx 5% complete for prog_iPAX7_Dox_rep3_1.gz
  Approx 5% complete for prog_iPAX7_Dox_rep3_2.gz
  Failed to process file prog_iPAX7_Dox_rep3_1.gz
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:158)
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
  	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
  	at java.base/java.lang.Thread.run(Thread.java:834)
  Failed to process file prog_iPAX7_Dox_rep3_2.gz
  uk.ac.babraham.FastQC.Sequence.SequenceFormatException: Midline 'BBBBBFFFFFFFFFFFFFFFFFFFFFFFFFB/77BF/' didn't start with '+'
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.readNext(FastQFile.java:172)
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.next(FastQFile.java:125)
  	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:77)
  	at java.base/java.lang.Thread.run(Thread.java:834)
    im a bit confused about what this error means, sis there something wrong with the fastq? im trying to replicate a study: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE150638 maybe some of the files were corrupted?
    s
    • 2
    • 1
  • s
    Hello everyone, I have sequencing data which is split in multiple lanes (L1, L2, L3, L4) for the same sample. Is there a way to specify these in a sample file so that they are considered as the same sample downstream for the HiC pipeline?
    s
    n
    • 3
    • 3
  • m
    Can I increase the running time. i have 4 samples in my sample sheet. each file size is ~ 50GB including R1 and R2.
    Copy code
    ERROR ~ Error executing process > 'NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (Patz1)'

Caused by:
  Process exceeded running time limit (16h)


Command executed:

  INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/\.rev.1.bt2$//"`
  [ -z "$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/\.rev.1.bt2l$//"`
  [ -z "$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
  
  bowtie2 \
      -x $INDEX \
      -U HiC_Patz1_7dpi_1.fastq.gz \
      --threads 12 \
      --un-gz Patz1_0_R1.unmapped.fastq.gz \
      --very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder \
      2> Patz1_0_R1.bowtie2.log \
      | samtools view -F 4 --threads 12 -o Patz1_0_R1.bam -
  
  if [ -f Patz1_0_R1.unmapped.fastq.1.gz ]; then
      mv Patz1_0_R1.unmapped.fastq.1.gz Patz1_0_R1.unmapped_1.fastq.gz
  fi
  
  if [ -f Patz1_0_R1.unmapped.fastq.2.gz ]; then
      mv Patz1_0_R1.unmapped.fastq.2.gz Patz1_0_R1.unmapped_2.fastq.gz
  fi
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN":
      bowtie2: $(echo $(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*$//')
      samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//')
      pigz: $( pigz --version 2>&1 | sed 's/pigz //g' )
  END_VERSIONS

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /media/manoj/Data/Manoj/Hi-C/nf-core-hic_2.1.0/2_1_0/work/cb/4acb2e3826060caafcb160ac0a2d00

Container:
  quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:a0ffedb52808e102887f6ce600d092675bf3528a-0

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- Check '.nextflow.log' file for details
    p
    s
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  • d
    Hi! I am trying to run the hic pipeline using apptainer instead of singularity. I run into the following error, which is not present using singularity. Other pipelines work with apptainer. Has someone tried this before? 🙂 Apptainer seems not to be able to pull containers, the timelimit is not reached, it fails more or less instantly. When i try to pull the containers manually both singularity and apptainer fail.
    Copy code
    dos02bi@gaia2:~/test3$ nextflow run nf-core/hic -r 2.1.0 -profile test,apptainer --outdir ./
Nextflow 24.10.1 is available - Please consider updating your version to it

 N E X T F L O W   ~  version 24.10.0

[...]

Pulling Apptainer image <docker://biocontainers/python:3.8.3> [cache /home/dos02bi/test3/work/singularity/biocontainers-python-3.8.3.img]
Pulling Apptainer image <docker://biocontainers/mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483:713df51cd897ceb893b9a6e6420f527d83c2ed95-0> [cache /home/dos02bi/test3/work/singularity/biocontainers-mulled-v2-c6ff206325681cbb9c9ef890bb8de554172c0483-713df51cd897ceb893b9a6e6420f527d83c2ed95-0.img]
Pulling Apptainer image <docker://biocontainers/samtools:1.16.1--h6899075_1> [cache /home/dos02bi/test3/work/singularity/biocontainers-samtools-1.16.1--h6899075_1.img]
Pulling Apptainer image <docker://biocontainers/bowtie2:2.4.4--py39hbb4e92a_0> [cache /home/dos02bi/test3/work/singularity/biocontainers-bowtie2-2.4.4--py39hbb4e92a_0.img]
WARN: Apptainer cache directory has not been defined -- Remote image will be stored in the path: /home/dos02bi/test3/work/singularity -- Use the environment variable NXF_APPTAINER_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK'

Caused by:
  Failed to pull singularity image
    command: apptainer pull  --name biocontainers-python-3.8.3.img.pulling.1732529258575 <docker://biocontainers/python:3.8.3> > /dev/null
    status : 255
    hint   : Try and increase apptainer.pullTimeout in the config (current is "20m")
    message:
      FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for <docker://biocontainers/python:3.8.3>: reading manifest 3.8.3 in <http://docker.io/biocontainers/python|docker.io/biocontainers/python>: requested access to the resource is denied



 -- Check '.nextflow.log' file for details
    👀 1
    ✅ 2
    m
    • 2
    • 9
  • y
    Hi, I used to use the pipeline but in December it was not working, I updated nextflow etc... but I have still this error with singularity :
    Copy code
    ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK'

Caused by:
  Failed to pull singularity image
    command: singularity pull  --name depot.galaxyproject.org-singularity-python-3.8.3.img.pulling.1736157705805 <https://depot.galaxyproject.org/singularity/python:3.8.3> > /dev/null
    status : 255
    hint   : Try and increase singularity.pullTimeout in the config (current is "20m")
    message:
      ERROR: pull is only supported for shub URIs
    s
    • 2
    • 10
  • m
    s
    • 2
    • 2
  • k
    Hi I'm running the hic test pipeline. Any tips for troubleshooting "ImportError: cannot import name 'is_categorical' from 'pandas.api.types' " ?
    Copy code
    nextflow run nf-core/hic -profile test,conda --outdir /home/floer/nf_test                                                    executor >  local (7)
[47/557dd9] NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv)                      [100%] 1 of 1 ✔
[bc/3b6050] NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (W303_SGD_2015_JRIU00000000.fsa)        [100%] 1 of 1 ✔
[f4/a8e314] NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (W303_SGD_2015_JRIU00000000.fsa) [100%] 1 of 1 ✔
[2a/cafb8d] NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)                   [100%] 1 of 1 ✔
[a6/cba38e] NFCORE_HIC:HIC:FASTQC (SRR4292758)                                                  [100%] 1 of 1 ✔
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS                                     -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED                          -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES                                  -
[-        ] NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION                                         -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION                                       -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_STATS                                                   -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS                                                  -
[cc/0c1892] NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})                                       [100%] 2 of 2, failed: 2 ✘
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_CLOAD                                                  -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_BALANCE                                                -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY                                                -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_DUMP                                                   -
[-        ] NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP                                             -
[-        ] NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS                                              -
[-        ] NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS                                       -
[-        ] NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION                                            -
[-        ] NFCORE_HIC:HIC:TADS:HIC_FIND_TADS                                                   -
[-        ] NFCORE_HIC:HIC:CUSTOM_DUMPSOFTWAREVERSIONS                                          -
[-        ] NFCORE_HIC:HIC:MULTIQC                                                              -
Execution cancelled -- Finishing pending tasks before exit

ERROR ~ Error executing process > 'NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})'

Caused by:
  Process `NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})` terminated with an error exit status (1)


Command executed:

  cooler makebins \
       \
      W303_SGD_2015_JRIU00000000.fsa.sizes \
      2000 > cooler_bins_2000.bed
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS":
      cooler: $(cooler --version 2>&1 | sed 's/cooler, version //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/bin/cooler", line 6, in <module>
      from cooler.cli import cli
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/__init__.py", line 14, in <module>
      from .api import Cooler, annotate
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/api.py", line 13, in <module>
      from .core import (
    File "/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/cooler/core.py", line 3, in <module>
      from pandas.api.types import is_categorical
  ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/home/floer/work/conda/env-cd84d045ac8cca6d16b389fcdb8d93bc/lib/python3.11/site-packages/pandas/api/types/__init__.py)

Work dir:
  /home/floer/work/0f/27c3e96b6a4de722b1cdd73e386a1a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- Check '.nextflow.log' file for details
    execution_report_2025-01-22_09-32-00.html
    s
    • 2
    • 1
  • a
    Hello! First message on this Slack, I'm new to nf-core & Nextflow. I'm running this pipeline offline, with a 
    --fasta
    genome and 
    --digestion hindiii
    . I've run into an issue where Bowtie2-based steps want the genome file to be bgzipped, but the 
    GET_RESTRICTION_FRAGMENTS
    step is unable to read the compressed file. Here's the full output:
    Copy code
    executor >  slurm (5)
[8b/2a51d4] NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet_hic.csv)    [100%] 1 of 1, cached: 1 ✔
[15/194ceb] NFCORE_HIC:HIC:PREPARE_GENOME:BOWTIE2_BUILD (hg38.bgzip.fa.gz)        [100%] 1 of 1, cached: 1 ✔
[a5/2f28f7] NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (hg38.bgzip.fa.gz) [100%] 1 of 1, cached: 1 ✔
[c0/aafef0] NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)     [100%] 1 of 1, failed: 1 ✘
[84/dae341] NFCORE_HIC:HIC:FASTQC (CHiC_CD34_rep2)                                [100%] 2 of 2, cached: 2 ✔
[69/348fb4] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN (CHiC_CD34_rep2)   [100%] 4 of 4 ✔
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:TRIM_READS                       -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:BOWTIE2_ALIGN_TRIMMED            -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:MERGE_BOWTIE2                    -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO_MAPPING:COMBINE_MATES                    -
[-        ] NFCORE_HIC:HIC:HICPRO:GET_VALID_INTERACTION                           -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_VALID_INTERACTION                         -
[-        ] NFCORE_HIC:HIC:HICPRO:MERGE_STATS                                     -
[-        ] NFCORE_HIC:HIC:HICPRO:HICPRO2PAIRS                                    -
[32/621d19] NFCORE_HIC:HIC:COOLER:COOLER_MAKEBINS (null})                         [100%] 3 of 3, cached: 3 ✔
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_CLOAD                                    -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_BALANCE                                  -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_ZOOMIFY                                  -
[-        ] NFCORE_HIC:HIC:COOLER:COOLER_DUMP                                     -
[-        ] NFCORE_HIC:HIC:COOLER:SPLIT_COOLER_DUMP                               -
[-        ] NFCORE_HIC:HIC:HIC_PLOT_DIST_VS_COUNTS                                -
[-        ] NFCORE_HIC:HIC:COMPARTMENTS:COOLTOOLS_EIGSCIS                         -
[-        ] NFCORE_HIC:HIC:TADS:COOLTOOLS_INSULATION                              -
Plus 2 more processes waiting for tasks…
-[nf-core/hic] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)'

Caused by:
  Process `NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS (A^AGCTT)` terminated with an error exit status (1)


Command executed:

  digest_genome.py -r A^AGCTT -o restriction_fragments.bed hg38.bgzip.fa.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_HIC:HIC:PREPARE_GENOME:GET_RESTRICTION_FRAGMENTS":
      python: $(echo $(python --version 2>&1) | sed 's/Python //')
  END_VERSIONS

Command exit status:
  1

Command output:
  Analyzing hg38.bgzip.fa.gz
  Restriction site(s) AAGCTT
  Offset(s) 1

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Environment variable SINGULARITYENV_SNIC_TMP is set, but APPTAINERENV_SNIC_TMP is preferred
  Traceback (most recent call last):
    File "/scale/gr01/shared/nf-core/nf-core-hic_2.1.0/2_1_0/bin/digest_genome.py", line 176, in <module>
      contig_names, all_indices = find_re_sites(filename, sequences, offset=offset)
    File "/scale/gr01/shared/nf-core/nf-core-hic_2.1.0/2_1_0/bin/digest_genome.py", line 32, in find_re_sites
      for line in infile:
    File "/usr/local/lib/python3.9/codecs.py", line 322, in decode
      (result, consumed) = self._buffer_decode(data, self.errors, final)
  UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
    The 
    digest_genome.py
    script tries to do an 
    open(filename, "r")
    , but since the file is compressed it gives the error above. I'm thinking the easiest way around this is to just provide a BED file with 
    --restriction_fragments
    directly? But I would love some advice on how to generate such a file. I'm not super familiar with Hi-C analysis in general. Thanks a lot!
    s
    • 2
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  • a
    Hello Everyone, I have been trying to use the .pairs files (output in 
    results/hicpro/valid_pairs/pairix
    ) for downstream analysis, but it seems that the pair files that i am generating don't have the proper header for the 4DN format. I believe that the header is not being generated at all in the 
    <http://hicpro2pairs.nf|hicpro2pairs.nf>
    module, but i am not too sure. Any help will be appreciated.
    Copy code
    ##columns: readID chr1 pos1 chr2 pos2 strand1 strand2
    awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs | bgzip -c > ${prefix}_contacts.pairs.gz
    ##sort -k2,2 -k4,4 -k3,3n -k5,5n ${prefix}_contacts.pairs | bgzip -c > ${prefix}_contacts.pairs.gz
    pairix -f ${prefix}_contacts.pairs.gz
    n
    • 2
    • 1
  • d
    Hi! When i try to run the hic pipeline it fails with the error to pull the samtools container. When i try to do it manually, it also fails. On dockerhub i seems like that version is no longer available.
    Copy code
    März-12 10:02:28.291 [Actor Thread 69] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_HIC:HIC:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (1); work-dir=null
  error [java.lang.IllegalStateException]: java.lang.IllegalStateException: Failed to pull singularity image
  command: apptainer pull  --name biocontainers-samtools-1.16.1--h6899075_1.img.pulling.1741770146007 <docker://biocontainers/samtools:1.16.1--h6899075_1> > /dev/null
  status : 255
  hint   : Try and increase apptainer.pullTimeout in the config (current is "20m")
  message:
    INFO:    /etc/singularity/ exists; cleanup by system administrator is not complete (see <https://apptainer.org/docs/admin/latest/singularity_migration.html>)
    FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for <docker://biocontainers/samtools:1.16.1--h6899075_1>: reading manifest 1.16.1--h6899075_1 in docker.io/biocontainers/samtools: manifest unknown
    https://hub.docker.com/r/biocontainers/samtools/tags?ordering=-last_updated
  • f
    Hello, is it possible to run the HIC pipe-line with micro-C generated data? thanks a lot, best, Greg
  • p
    Hello, is it possible to run the HI-C pipeline with micro-C data? thanks
  • s
    @nservant, are you able to answer that?
  • n
    Hi, yes absolutely
  • n
  • n
    you can run it with the 
    --dnase
    option, that's the same
  • n
    in the next version, we will update this parameter to make it clearer
  • f
    Amazing! thank you very much !
  • e
    Hi all, what is the most recent version of Nextflow that the nf-core #CJ3UVAZFT pipeline works with for HindIII digestion? I seem to be getting stuck at the FASTQC stage where no further processes are being submitted or even beginning with version 25.04.8?
  • e
    Hi all! Does the hic pipeline works for you at the moment, the most recent release 2.1.0 ? I am just trying to set up nextflow for the first time, using all most recent versions of nextflow 25.10.3 and apptainer 1.4.5 and it is impossible to pull the containers. I’ve tried everything and made sure that my softwares and configs are correct.
    Copy code
    -[nf-core/hic] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_HIC:HIC:INPUT_CHECK:SAMPLESHEET_CHECK'

Caused by:
  Failed to pull singularity image
    command: apptainer pull  --name biocontainers-python-3.8.3.img.pulling.1764791847785 <docker://biocontainers/python:3.8.3> > /dev/null
    status : 255
    hint   : Try and increase apptainer.pullTimeout in the config (current is "20m")
    message:
      FATAL:   While making image from oci registry: error fetching image to cache: failed to get checksum for <docker://biocontainers/python:3.8.3>: reading manifest 3.8.3 in <http://docker.io/biocontainers/python|docker.io/biocontainers/python>: requested access to the resource is denied
    Is there a way to check if the urls for the images provided in the pipeline are correct? Does anyone else struggles with this too? Thank you!
    s
    a
    • 3
    • 16
  • s
    Hi, @Felipe Almeida and I are planning an in-person local hub in Copenhagen for the #C0ACF0TPF5E and I think it would be a good idea to have a project to work on some of #CJ3UVAZFT issues. Just wanted to mention this here so we don't overlap in case anyone is planning something similar. We'll be working out the details soon, if anyone wants to join. 🙂
    🎉 3
    p
    t
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  • h
    Hello everyone, i guess this project is only takes place in person and not online ? Thank you!
    👋 1
    p
    f
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  • s
    Hi, @Thibault Poinsignon @nservant. 😁 We have some fixes dependent on https://github.com/nf-core/hic/pull/236, which seems to pass all checks. Do you think it could already be merged?
    👀 2
    t
    • 2
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  • f
    I'm new to HiC, here is my newcomer questions / suggestions about https://nf-co.re/hic/2.1.0/parameters/: for the 
    --restriction_fragments
    flag the help text says: "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the —restriction_site option". It seems to me that setting 
    --digestion
    also sets the 
    —restriction_site
    option, and hence the help text could say: "This file depends on the Hi-C protocols and digestion strategy. If not provided, the pipeline will build it using the --digestion or —restriction_site option"? Also, do I understand correctly that 
    --restriction_site
    and 
    --ligation_site
    are set automatically if you set 
    --digestion
    ? If yes, then a short help text there would also be nice. I'm happy to do a PR :)
    p
    s
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  • d
    Hello, I'm using the nf-core/hic pipeline to process some public Hi-C datasets. While I was using the pipeline, I noticed that it copies output files independently of the parameter 
    publish_dir_mode
    . For context, I normally change nf-core's default 
    copy
    mode to 
    link
    or 
    symlink
    to avoid storage duplication and at the same time maintain the ability to resume. I reviewed the pipeline's code in GitHub and have noticed that 
    hic/conf/modules.config
    has all processes hardcoded with publishDir 
    mode: 'copy'
    in the latest stable version 2.1.0. For the 
    dev
    version, most processes also have 
    mode: 'copy'
    , except for 
    MULTIQC
    . As it stands now, nf-core/hic always copies results to the output directory ignoring the parameter 
    publish_dir_mode
    , which isn't ideal. Please let me know if I'm missing something obvious. But if I'm not, I'll be happy to change the code myself and do a Pull Request.
    s
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  • b
    Request for updating the release tag, and updating the master branch for the new parser. I am willing to help any way I can. There are also a lots of issues that needs to be addressed too.
  • p
    This pipeline would definitely benefit from some maintenance work 💯 @Benson - if you're willing and able to help that would be great! The beauty of nf-core is that anyone can jump in and work on pipelines.
    100 rainbow 1
    b
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