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When a bed file is provided using the -blacklist parameter the pipeline stops throwing the exception below:
bed
-blacklist
Invalid method invocation `pow` with arguments: 2 (java.lang.Integer), [:] (groovy.util.ConfigObject) on Math type
As reported in slack.
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
The text was updated successfully, but these errors were encountered:
Closed in favour of #268
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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: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
The text was updated successfully, but these errors were encountered: