Biowulf High Performance Computing at the NIH
distiller-nf on Biowulf

A modular Hi-C mapping pipeline for reproducible data analysis, it was used for Micro-C analysis too. The distiller pipeline aims to provide the following functionality:

  • Align the sequences of Hi-C molecules to the reference genome
  • Parse .sam alignment and form files with Hi-C pairs
  • Filter PCR duplicates
  • Aggregate pairs into binned matrices of Hi-C interactions


    • Krietenstein N, Abraham S, Venev SV, Abdennur N, Gibcus J, Hsieh TS, Parsi KM, Yang L, Maehr R, Mirny LA, Dekker J, Rando OJ. Ultrastructural Details of Mammalian Chromosome Architecture. Mol Cell. 2020 May 7 PubMed |  Journal
    Important Notes
    • Module Name: distiller-nf (see the modules page for more information)
    • distiller-nf is a nextflow pipeline, it requires three configuration files: project.yml(for input and ref seq), nextflow.config(already setted up on Biowulf), and local/cluster.config(Biowulf provides templates which you can download and modify).
      	cp -r ${DISTILLER_CONFIG:-none} .
    • Then to give a customized config file, you have to provide the full path to custom.config.
      	-profile custom --custom_config /your_full_path_to/custom.config
    • To run test data with test_project.yml, you also need to save a local copy of the test data.
      	cp -r ${DISTILLER_TEST_DATA:-none} .

    Interactive job
    Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

    Allocate an interactive session and run the program.
    Sample session (user input in bold):

    [user@biowulf]$ sinteractive --cpus-per-task=10 --mem=10G
    salloc.exe: Pending job allocation 46116226
    salloc.exe: job 46116226 queued and waiting for resources
    salloc.exe: job 46116226 has been allocated resources
    salloc.exe: Granted job allocation 46116226
    salloc.exe: Waiting for resource configuration
    salloc.exe: Nodes cn3144 are ready for job
    [user@cn3144]$ module load distiller-nf
    [user@cn3144]$ mkdir /data/$USER/distiller/
    [user@cn3144]$ cd /data/$USER/distiller/
    [user@cn3144]$ cp -r ${DISTILLER_TEST_DATA:-none} .
    [user@cn3144]$ cp -r ${DISTILLER_CONFIG:-none} .
    [user@cn3144]$ nextflow $DISTILLER/ -params-file ./test/test_project.yml
    N E X T F L O W  ~  version 21.04.1
    Launching `/usr/local/apps/distiller-nf/0.3.3/` [trusting_euler] - revision: a0539e1286
    executor >  local (26)
    [-        ] process > download_truncate_chunk_fastqs                                      -
    [-        ] process > local_truncate_chunk_fastqs                                         -
    [-        ] process > fastqc                                                              -
    [a8/eb3aac] process > map_parse_sort_chunks (library:MATa_R1 run:lane1 chunk:0)           [100%] 5 of 5 ✔
    [0e/e85c28] process > merge_dedup_splitbam (library:MATa_R2)                              [100%] 4 of 4 ✔
    [50/2f4035] process > bin_zoom_library_pairs (library:MATa_R2 filter:mapq_30)             [100%] 8 of 8 ✔
    [d1/bd0918] process > merge_zoom_library_group_coolers (library_group:all filter:mapq_30) [100%] 6 of 6 ✔
    [3a/d421e5] process > merge_stats_libraries_into_groups (library_group:MATalpha)          [100%] 3 of 3 ✔
    Completed at: 04-Aug-2021 12:44:36
    Duration    : 1m 14s
    CPU hours   : 0.5
    Succeeded   : 26
    [user@cn3144]$ exit
    salloc.exe: Relinquishing job allocation 46116226
    [user@biowulf ~]$

    Batch job
    Most jobs should be run as batch jobs.

    Create a batch input file (e.g. For example:

    set -e
    module load distiller-nf
    cd /data/$USER/distiller/
    cp -r ${DISTILLER_TEST_DATA:-none} .
    cp -r ${DISTILLER_CONFIG:-none} .
    nextflow $DISTILLER/ -params-file ./test/test_project.yml -profile cluster

    Submit this job using the Slurm sbatch command.