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Bed file provided using the --blacklist parameter triggers an error #289

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JoseEspinosa opened this issue Jun 8, 2023 · 1 comment
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@JoseEspinosa
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Description of the bug

When a bed file is provided using the -blacklist parameter the pipeline stops throwing the exception below:

Invalid method invocation `pow` with arguments: 2 (java.lang.Integer), [:] (groovy.util.ConfigObject) on Math type

As reported in slack.

Command used and terminal output

nextflow run nf-core/atacseq -r 2.0 --input samplesheet.csv --genome homo_sapiens.GRCh38.release_102 -config /public/singularity/containers/nextflow/lmb-nextflow/lmb.config --read_length 100 --aligner bowtie2 --deseq2_vst --outdir results --mito_name MT --blacklist ENCFF356LFX.bed -bg
NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (preB_aged_REP4_T1)
[5a/aa461e] Submitted process > NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (proB_young_REP1_T1)
[60/242e95] Submitted process > NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (preB_young_REP1_T1)
Invalid method invocation `pow` with arguments: 2 (java.lang.Integer), [:] (groovy.util.ConfigObject) on Math type
-[nf-core/atacseq] Pipeline completed with errors-
WARN: Killing running tasks (8)
[a3/b730e5] Submitted process > NFCORE_ATACSEQ:ATACSEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (proB_aged_REP1_T1)


### Relevant files

_No response_

### System information

Nextflow version 22.10.7
@JoseEspinosa JoseEspinosa added the bug Something isn't working label Jun 8, 2023
@JoseEspinosa JoseEspinosa added this to the 2.1 milestone Jun 8, 2023
@JoseEspinosa JoseEspinosa self-assigned this Jun 8, 2023
@JoseEspinosa JoseEspinosa added WIP Work in progress duplicate This issue or pull request already exists and removed bug Something isn't working WIP Work in progress labels Jun 8, 2023
@JoseEspinosa
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Closed in favour of #268

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