Special character in filename fix

[yashpatel6]

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Adding fix for intermediate file deletion where filenames containing special characters results in an error during deletion.

Testing Results

Tested with convert-BAM2FASTQ, log and output here: /hot/software/pipeline/pipeline-convert-BAM2FASTQ/Nextflow/development/unreleased/yashpatel-handle-special-characters/run.log

[nwiltsie]

The changes look fine, although I'm curious about what triggered the issue in the first place - where did a filename with special characters come from?

[yashpatel6]

The changes look fine, although I'm curious about what triggered the issue in the first place - where did a filename with special characters come from?

There are cases where intermediate files are named based on metadata found in file headers and that results in special characters being carried into the filenames. Ex. splitting a BAM per readgroup where a readgroup ID has a special character (ID:my:id - the ID would contain :) would result in the file having that character in the name