mkfastq fails on AWS Batch

[KallyopeComp]

Description of the bug

Thank you for preparing a helpful tool to standardize genomics workflows. There is a small issue with running the pipeline using AWS Batch with mkfastq.

Some of the required output directories from the CellRanger output are empty, leading the pipeline to raise an error. For the test data *_outs/outs/fastq_path/Reports is empty. Possibly *_outs/outs/fastq_path/Stats is empty in other cases (I'm not sure).

At least, line 13 should be modified to read:
tuple val(meta), path("*_outs/outs/fastq_path/Reports") , optional:true, emit: reports
Possibly line 14 should be modified as well to:
tuple val(meta), path("*_outs/outs/fastq_path/Stats") , optional:true, emit: stats

With these changes, the pipeline completes successfully.

Command used and terminal output

$ nextflow run demultiplex -profile docker -config ../nextflow.config --skip_tools samshee,falco,fastp --input test_pipeline_samplesheet.csv --demultiplexer mkfastq --outdir {private s3 directory}

Relevant part of the terminal output:
ERROR ~ Error executing process > 'NFCORE_DEMULTIPLEX:DEMULTIPLEX:MKFASTQ_DEMULTIPLEX:CELLRANGER_MKFASTQ (test_sample.1)'

Caused by:
Missing output file(s) *_outs/outs/fastq_path/Reports expected by process NFCORE_DEMULTIPLEX:DEMULTIPLEX:MKFASTQ_DEMULTIPLEX:CELLRANGER_MKFASTQ (test_sample.1)

Relevant files

Archive includes the pipeline samplesheet (which specifies test data from 10X), a nextflow.config (which specifies AWS Batch executor), and the nextflow log
Archive.zip

System information

Nextflow Version: 24.04.4
Hardware: Cloud (AWS batch with custom AMI built as described in the Nextflow documentation)
Executor: AWS BAtch
Container engine: Docker
OS: Launched from machine Ubuntu 22.04, AMI uses Amazon Linux 2
Version of nf-core/demultiplex: Latest master branch, commit ebefeef