No such variable CUTADAPT (v.2.2.0)

[joannakraw]

Description of the bug

Problem description:

I encountered an error while running the pipeline with the cutadapt option, specifically when passing adapter sequences using the five_prime_adapter and three_prime_adapter parameters. The pipeline execution fails with the following error message:

ERROR ~ No such variable: CUTADAPT

 -- Check script '/pod-data/pipelines/new_crisprseq/with_error/crisprseq/./workflows/crisprseq_screening.nf' at line: 89 or see '.nextflow.log' file for more details

Workaround:

I have resolved this issue locally by making the following changes:

• Replaced CUTADAPT.out with CUTADAPT_FIVE_PRIME in line 89.
• Replaced CUTADAPT.out with CUTADAPT_THREE_PRIME in line 98.
  These modifications allowed the pipeline to run without encountering the No such variable error. I attach the whole fragment of the modified code below:

Modified code

In the workflows/crisprseq_screening.nf:

        //set adapter seq to null to make it compatible with crispr targeted
        ch_cutadapt = ch_input.combine(Channel.value([[]]))
        if(params.five_prime_adapter) {
            CUTADAPT_FIVE_PRIME(
                ch_cutadapt
            )
            CUTADAPT_FIVE_PRIME.out.reads.combine(Channel.value([[]])).set { ch_cutadapt }
            ch_cutadapt.map{ meta, fastq, proto  ->
                meta.id = "${meta.id}_trim"
                [meta, fastq, proto]
            }.set { ch_cutadapt }

            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_FIVE_PRIME.out.log.collect{it[1]})
            ch_versions = ch_versions.mix(CUTADAPT_FIVE_PRIME.out.versions)
        }

        if(params.three_prime_adapter) {
            CUTADAPT_THREE_PRIME(
                ch_cutadapt
            )
            ch_cutadapt = CUTADAPT_THREE_PRIME.out.reads.combine(Channel.value([[]]))
            ch_multiqc_files = ch_multiqc_files.mix(CUTADAPT_THREE_PRIME.out.log.collect{it[1]})
            ch_versions = ch_versions.mix(CUTADAPT_THREE_PRIME.out.versions)
        }

Command used and terminal output

nextflow run main.nf -profile k8s,docker -params-file parameters.json

ERROR ~ No such variable: CUTADAPT

 -- Check script '/pod-data/pipelines/new_crisprseq/with_error/crisprseq/./workflows/crisprseq_screening.nf' at line: 89 or see '.nextflow.log' file for more details

Relevant files

No response

System information

Nextflow info:

• Version: 23.10.0 build 5889
• Created: 15-10-2023 15:07 UTC
• System: Linux 6.1.0-12-amd64
• Runtime: Groovy 3.0.19 on OpenJDK 64-Bit Server VM 17.0.8+7-LTS
• Encoding: UTF-8 (UTF-8)

[LaurenceKuhl]

Hi @joannakraw
thank you so much!! Would you actually mind opening a PR with your contribution? If you're unsure how to go about it i would be happy to help!
Laurence

[joannakraw]

Hi @LaurenceKuhl, thanks for such a quick reply! I will try to do this, and let you know in case of any problems.
Best,
Joanna

[LaurenceKuhl]

Hi Joanna,

Thanks!! don't hesitate to just open it and tag me if you have any questions :)

[LaurenceKuhl]

Hi @joannakraw, could you let me know why you re opened this? thanks!

[joannakraw]

Hi @LaurenceKuhl, I've clicked close by mistake, so I've reopened it again. I didn't know if I'm supposed to close this issue or you, sorry for the confusion!

[LaurenceKuhl]

All good :D I'll close it again, unless you are still experiencing issues even with your bug fix then please re-open it :)