CAT_FASTQ does not work with single end data
roberta-davidson opened this issue · comments
roberta-davidson commented
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