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# mnaseseq
  • m
    Hi <!channel>, as you probably know already we have a coming hackathon code This edition will be focused on documentation 🗃️ And we need your help 🙏 If you feel like this pipeline is missing any documentation, can you please make a GitHub issue on its repo with the 
    documentation
    label. We will sort out if it's dependent on the template or the pipeline itself and populate the hackathon project board accordingly. Thanks a lot for your help, On behalf of the hackathon organizing team nf core socks Maxime
  • a
    hi all, I am currently testing the mnaseseq pipeline:
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    # check that the most updated version is used:
nextflow pull nf-core/mnaseseq
    Checking nf-core/mnaseseq ...
    Already-up-to-date - revision: d7da403281 [dev]
    Copy code
    #run nfcore in test mode:
nextflow run nf-core/mnaseseq -profile test -r dev
nextflow run nf-core/mnaseseq -profile test,singularity -r dev
    both approaches produce an error:
    No such variable: ch_design_reads_csv
    Testing nf-core/rnaseq with the same configuration worked fine. Have you seen this before? I would really appreciate your insight.
  • h
    Hi @Adrija Kalvisa can you add 
    -dsl1
    to the command and use the latest release of NF please?
  • h
    The pipeline was written in Nextflow DSL1 and the latest version of NF assumes that the pipeline is written in DSL2. This should be auto-detected in future releases of NF.
  • a
    Thanks! I did
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    nextflow self-update
    CAPSULE: Downloading dependency io.nextflownf commonsjar:22.04.2
    CAPSULE: Downloading dependency io.nextflownf httpfsjar:22.04.2
    CAPSULE: Downloading dependency io.nextflownextflowjar:22.04.2
    N E X T F L O W
    version 22.04.2 build 5701
    created 16-05-2022 17:52 UTC (19:52 CEST)
    cite doi:10.1038/nbt.3820
    http://nextflow.io
    then run
    Copy code
    nextflow run nf-core/mnaseseq -profile test,singularity -r dev -dsl1
    This time the error message is the following:
    Execution cancelled -- Finishing pending tasks before exit
    -[nf-core/mnaseseq] Pipeline completed with errors-
    Error executing process > ‘TrimGalore (DEGRON_R2_T1)’
    Caused by:
    Process 
    TrimGalore (DEGRON_R2_T1)
    terminated with an error exit status (1)
    Command executed:
    [ ! -f DEGRON_R2_T1_1.fastq.gz ] && ln -s NGS-13237_S2_L006_R1_001.fastq.gz DEGRON_R2_T1_1.fastq.gz
    [ ! -f DEGRON_R2_T1_2.fastq.gz ] && ln -s NGS-13237_S2_L006_R2_001.fastq.gz DEGRON_R2_T1_2.fastq.gz
    trim_galore --cores 4 --paired --fastqc --gzip DEGRON_R2_T1_1.fastq.gz DEGRON_R2_T1_2.fastq.gz
    Command exit status:
    1
    Command output:
    (empty)
    Command error:
    Cutadapt version: 1.18
    Could not detect version of Python used by Cutadapt from the first line of Cutadapt (but found this: >>>#!/bin/sh<<<)
    Letting the (modified) Cutadapt deal with the Python version instead
    Parallel gzip (pigz) detected. Proceeding with multicore (de)compression using 4 cores
    And looking into the 
    DEGRON_R2_T1_1.fastq.gz_trimming_report.txt
    :
    ERROR: Running in parallel is not supported on Python 2
    Furthermore, The only image stored at my local singularity cache after running the pipeline is this: 
    nfcore-mnaseseq-dev.img
  • h
    Copy code
    process {
    withName: TrimGalore {
        cpus = 1
    } 
}
  • h
    Weird. Can you try putting the contents above in a file called 
    custom.config
    and pass on the CLI with 
    -c custom.config
    ?
  • a
    This worked, thank you!
    👍🏽 1
  • y
    Hi, I am wondering if a stable version of mnaseseq would be released soon. @hpatel Thank you!
  • h
    Hi @Yunhui Peng! Have you tested 
    dev
    and it is working for you?
  • h
    I definitely won't have time to update the pipeline to current standards but I can push a stable tagged release for you to cite if required.
  • y
    Hi @hpatel, Yes, it works well for me. It will be great if a stable tagged release could be included. Thank you very much!
  • h
    Done:
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    nextflow run nf-core/mnaseseq -profile test,docker -r 1.0.0
  • h
    I pushed the containers for 1.0.0 manually and the above command is working for me locally so should be all good
  • h
    I also slipped in this bit in the config so the pipeline works with more recent versions of NF (until DSL1 is auto-detected that is): https://github.com/nf-core/mnaseseq/blob/eb5ea5c9b122f2cc29810e6a040187838bda6702/nextflow.config#L8-L10
  • h
    Apologies for the delay in getting this out but hopefully it helps you cite a stable version.
  • y
    Thank you! @hpatel
  • p
  • p
    @Theodoros Georgomanolis ☝🏻
  • h
    ✅ 1
  • t
    @hpatel that worked. Thank you. Any idea if this will be resolved? is the mnase pipeline being further developed?
  • t
    I mean it is weird because it throughs also this python2 version error. Maybe this is a singularity "error", that needs for the singularity image to be updated
  • p
  • u
    Is there any update plan for this pipeline?👀
  • h
    Hi, is this channel still active? Could I ask some questions please?
    m
    • 2
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  • h
    Thanks, I wonder if anyone has worked with DANPOS. I ran the pipeline successfully but now I am a bit confused about danpos
  • j
    Hi! This pipeline didn't get a template update with tools 3.0.0 due to a missing 
    .nf-core.yml
    file. Please check the [nf-core/tools documentation](https://nf-co.re/tools) for the correct format. Once you changed that in your 
    dev
    branch you can get a template sync PR by starting the sync GHA action with your pipeline name as an input https://github.com/nf-core/tools/actions/workflows/sync.yml
    👀 1
    m
    • 2
    • 1
  • m
    <!channel> sorry, just wondering if anyone is running this pipeline, I might have found a person interested in continuing the development of this pipeline (or at least trying to update to DSL2)
    s
    t
    c
    • 4
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  • g
    Hello, I've created a new issue to update this pipeline to DSL2. Join me if you are interested. Here is the issue https://github.com/nf-core/mnaseseq/issues/49#issue-3876208482.
  • r
    Hi, I would like to help in development of this pipeline. Please let me know which one is the development branch?
    m
    g
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    • 7