Describe the bug
If you provide bam files without specifying --bam and skip earlier steps - processes will start running but start failing due to tag ${file.baseName} not correctly finding right type of input files.
Proposed solution
Add a check that the file suffixes correspond to the expected parameter specifications.
fastq: .fastq.gz, fastq, fq.gz, .fq
bam: .bam
Suggestion from @maxibor: combine a filter (e.g. .filter { it =~/.*.bam/} with ifEmpty.
Describe the bug
If you provide bam files without specifying
--bamand skip earlier steps - processes will start running but start failing due totag ${file.baseName}not correctly finding right type of input files.Proposed solution
Add a check that the file suffixes correspond to the expected parameter specifications.
fastq: .fastq.gz, fastq, fq.gz, .fq
bam: .bam
Suggestion from @maxibor: combine a filter (e.g.
.filter { it =~/.*.bam/}withifEmpty.