Speed up strip_input_fastq process

[maxibor]

Rewrite of extract_map_reads.py to speed it up and make it more robust:

• Fastq parsing now handled by Biopython
• Fastq I/O now handled with xopen
• Now handles better forward and reverse reads files.
• Lowers resources requirements for strip_input_fastq

Speed improvement

Wall time before (strip_input_fastq in green):

Wall time after (strip_input_fastq in lightblue):

PR checklist

• This comment contains a description of changes (with reason)
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• CHANGELOG.md is updated

Learn more about contributing: https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md

[jfy133]

I don't see any issue code wise. I will run a big test on sdag to double check then will merge.

[jfy133]

Looks good, mybig test shows massive improvement.

One small request: please move the publishDir outside samtools/. An independent directory is valid IMO.

Then we are good for merging!

[maxibor]

Looks good, mybig test shows massive improvement.

One small request: please move the publishDir outside samtools/. An independent directory is valid IMO.

Then we are good for merging!

Done

[jfy133]

Merging - strip_fastq passes, tests hung on GATK UG Download which happens sometimes.