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nf-core / mag

Assembly and binning of metagenomes
https://nf-co.re/mag
MIT License
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CAT_FASTQ does not work with single end data #557

Closed roberta-davidson closed 7 months ago

roberta-davidson commented 8 months ago

Description of the bug

strange pipeline error likely caused by single end data input - as suggested by @jfy133 on slack

Command used and terminal output

nextflow run nf-core/mag -r 2.5.1 \
        -profile singularity \
        --outdir /hpcfs/users/a1717363/micro_func/results \
        --input samplesheet.csv \
        --single_end TRUE \
        --reads_minlegth 15 \
        --megahit_options="--presets meta-large" \
        --skip_spades \
        --skip_spades_hybrid \
        --binning_map_mode own \
        --min_contig_size 1500 \
        --bowtie2_mode="--very-sensitive" \
        --binqc_tool busco \
        --skip_concoct \
        --refine_bins_dastool \
        --run_gunc \
        --ancient_dna \
        --pydamage_accuracy 0.5

Terminal output:

-[nf-core/mag] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_MAG:MAG:MEGAHIT (1)'

Caused by:
  Not a valid path value type: java.util.ArrayList ([hpcfs, users, a1717363, micro_func, work, 50, 247646ca18440e32b1e9237f1c2622, file.merged.fastq.gz])

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details


### Relevant files

[nextflow.log](https://github.com/nf-core/mag/files/13944074/nextflow.log)

### System information

nextflow version 23.10.0.5889
HPC
slurm
Singularity/3.10.5
nf-core/mag -r 2.5.1