BAMS folder is only saved if --igv flag is set

[meganbkratz]

Operating System

Other Linux (please specify below)

Other Linux

Red Hat Enterprise Linux 8.10

Workflow Version

v1.6.0

Workflow Execution

Other (please describe)

Other workflow execution

Slurm workload manager on a cluster

EPI2ME Version

No response

CLI command run

Command1 that doesn't output BAMS folder (or .bam/.bai files):

nextflow run epi2me-labs/wf-transcriptomes \
--fastq long_read_data/ \
--ref_genome reference/hg38/genome.fa \
--transcriptome-source reference-guided \
--ref_annotation reference/hg38/genes.gtf \
-profile singularity \
--out_dir output \
--sample_sheet long_read_data/sample_sheet.csv

Command2 that does output BAMS folder (with .bam/.bai files):

nextflow run epi2me-labs/wf-transcriptomes \
--fastq long_read_data/ \
--ref_genome reference/hg38/genome.fa \
--transcriptome-source reference-guided \
--ref_annotation reference/hg38/genes.gtf \
-profile singularity \
--igv \
--out_dir output_igv \
--sample_sheet long_read_data/sample_sheet.csv

Workflow Execution - CLI Execution Profile

None

What happened?

When I run Command 1 above, I don't see a BAMS directory in the output folder, or .bam or .bai files saved anywhere in the output directory. However, when I run command 2, which adds the --igv flag, the .bam and.bai files are saved in the BAMS directory in the output folder.

I'm not sure whether this is the intended behavior or not, but if it is, it's not clear from the documentation. The current documentation led me to expect the BAMS directory to be saved and populated regardless of what other flags were set.

Relevant log output

This file is big and I don't think it's super relevant, but if you want it anyway, please let me know.

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

other (please describe below)

Other demo data information

First, I had to make a couple adjustments (detailed below) to the example command script to have it run correctly, but then I saw the same issue I described above: unless the --igv flag is set, no BAMS directory is created and no .bam/.bai files were saved.

The two adjustments I had to make were:
1) change -profile standard to -profile singularity (this is expected since I'm running on a cluster that doesn't use docker)
2) delete "--minimap2_index_opts '-k15'" from the command -- whenever this was included I got the error:
Unknown option: -k15 -- Check the available commands and options and syntax with 'help'
(I also got a similar error when I changed it to -k14)

[nrhorner]

Closing as duplicate of #126