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nextflow is interpreting some command line option values as booleans when should be strings

Status: Open.

#12 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Jun 22, 2026

shouldn't convert bam to sam

Status: Open.

#11 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Jun 19, 2026

consider samplesheet input

enhancementNew feature or requestNew feature or request

Status: Open.

#10 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Jun 12, 2026

Document how sample IDs are determined from fastq file names

Status: Open.

#9 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Jun 4, 2026

Switch to latest nextflow features and syntax

Status: Open.

#6 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Apr 20, 2026

The pipeline does not check that sample IDs on sample sheet and sample IDs from fastq file names are concordant

Status: Open.

#1 In stenglein-lab/remapping_workflow;

· stenglein-lab opened on Sep 4, 2024