# ERROR ~ No such variable: ch\_multiqc\_report when trying to skip multiqc

**URL:** <https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494>\
**Category:** Ask for help\
**Tags:** nextflow, multiqc, nf-core\
**Created:** [December 31, 2025, 1:58pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494 "2025-12-31T13:58:59Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![sky5198](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/sky5198/32/2205_2.png) [@sky5198](https://community.seqera.io/u/sky5198)\
**Post date:** [December 31, 2025, 1:58pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/1 "2025-12-31T13:58:59Z")

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I am trying processing ChIP-sequencing data using Nextflow. I am trying to skip the multiqc step as it is giving me some trouble by adding the `--skip_multiqc` parameter to the command line. However, the process errors out pretty quickly. I have included my command line and the error message below. I was wondering if anyone had any insights. I have tried to run this with Nextflow v23.10.0 and then again with the updated v25.10.2.

Code:

```bash
#set up cache directory

NXF_SINGULARITY_CACHEDIR=/vscratch/singularity-cache

#command line

nextflow run nf-core/chipseq --skip_multiqc --input /vscratch/nf_chipProccessing/samplesheet/samplesheet.csv --outdir /vscratch/nf_chipProccessing/results --genome GRCm38 --narrow_peak --read_length 50 -profile singularity

```

Error message: `ERROR ~ No such variable: ch_multiqc_report`

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<div class="post-metadata">

**Author:** ![bentsherman](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/bentsherman/32/52_2.png) [@bentsherman](https://community.seqera.io/u/bentsherman)\
**Post date:** [January 1, 2026, 4:37pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/2 "2026-01-01T16:37:26Z")

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I took a quick look at the pipeline code. It looks like a bug on `master` that has been fixed in `dev`. So you can either use the `dev` branch or wait for the next pipeline release. You can check the chipseq repo to be sure

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<div class="post-metadata">

**Author:** ![yinshiyi](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/yinshiyi/32/1091_2.png) [@yinshiyi](https://community.seqera.io/u/yinshiyi)\
**Post date:** [January 2, 2026, 7:05pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/4 "2026-01-02T19:05:31Z")

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Hi @sky5198 ,

could you please try running with `-r dev`

```auto
nextflow run nf-core/chipseq -r dev –skip_multiqc --input /vscratch/nf_chipProccessing/samplesheet/samplesheet.csv --outdir /vscratch/nf_chipProccessing/results --genome GRCm38 --narrow_peak --read_length 50 -profile singularity

```

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<div class="post-metadata">

**Author:** ![sky5198](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/sky5198/32/2205_2.png) [@sky5198](https://community.seqera.io/u/sky5198)\
**Post date:** [January 2, 2026, 7:40pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/5 "2026-01-02T19:40:52Z")

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Thank you for the suggestion! Adding the `-r dev` did help me get further along. For clarification, I am now using nf-core/chipseq 2.2.0dev and Nextflow version 25.12.0-edge. However, I am now running into an issue where bedtools can’t create a temporary file. I feel like it might have something to do with how the scratch or temporary directory is set up. I have ran `export NXF_SINGULARITY_CACHEDIR= vscratch/nf-Six1/nf_chipProccessing` but it still can’t create the directory. I changed where the cache was going from my original code and there is plenty of storage available.

```auto
ERROR \~ Error executing process > 'NFCORE_CHIPSEQ:CHIPSEQ:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV (Input_DUC_REP1)'
Caused by:
  Process \`NFCORE_CHIPSEQ:CHIPSEQ:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV (Input_DUC_REP1)\` terminated with an error exit status (2)

Command executed:

  bedtools \\
      genomecov \\
      -ibam Input_DUC_REP1.mLb.clN.sorted.bam \\ -pc -bga -scale 0.0169010510 -bg \\ | LC_ALL=C sort --parallel=1 --buffer-size=3G -k1,1 -k2,2n \\ > Input_DUC_REP1.mLB.clN.bedGraph cat <<-END_VERSIONS > versions.yml "NFCORE_CHIPSEQ:CHIPSEQ:BAM_BEDGRAPH_BIGWIG_BEDTOOLS_UCSC:BEDTOOLS_GENOMECOV": bedtools: $(bedtools --version | sed -e "s/bedtools v//g") END_VERSIONS

Command exit status: 2
Command output: (empty)                               
Command error: sort: cannot create temporary file in '/scratch/22974174': No such file or directory
Work dir: /vscratch/nf_chipProccessing/work/c1/d295f5376638efcfdf48dae42f0f28           
Container: /vscratch/nf-Six1/nf_chipProccessing/work/singularity/community.wave.seqera.io-library-bedtools_coreutils-a623c13f66d5262b.img

```

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<div class="post-metadata">

**Author:** ![yinshiyi](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/yinshiyi/32/1091_2.png) [@yinshiyi](https://community.seqera.io/u/yinshiyi)\
**Post date:** [January 7, 2026, 7:06pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/6 "2026-01-07T19:06:00Z")

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This could be the a HPC setup issue.

`/scratch/22974174` looks like a HPC scratch/job\_id  
could be from `export TMPDIR=/scratch/$SLURM_JOB_ID`

My idea is to overwrite the TMPDIR definition to use the workDir defined in nextflow. Not sure if the following is going to work, but you could try adding this into your nextflow config

```groovy
process {
    env.TMPDIR = “${task.workDir}”
}

```

Also have you run this pipeline successfully before on your HPC? If you have run other nf-core pipeline successfully before, you could try to compare the `nextflow.config` files.

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<div class="post-metadata">

**Author:** ![sky5198](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/sky5198/32/2205_2.png) [@sky5198](https://community.seqera.io/u/sky5198)\
**Post date:** [January 11, 2026, 11:52pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/7 "2026-01-11T23:52:52Z")

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Thank you everyone for the help! I have found that if I use nextflow version 23.10.0, nf-core/chipseq v2.1.0 and update MultiQC to 1.33, I can run the pipeline straight through without any errors. I will keep in mind overwriting the TMPDIR because that might be useful if I run into issues in the future.

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<div class="post-metadata">

**Author:** ![system](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/system/32/2402_2.png) [@system](https://community.seqera.io/u/system)\
**Post date:** [January 18, 2026, 11:53pm UTC](https://community.seqera.io/t/error-no-such-variable-ch-multiqc-report-when-trying-to-skip-multiqc/2494/8 "2026-01-18T23:53:28Z")

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