Fix when multiple PacBio files are given

[muffato]

The bug occurred when there were multiple PacBio files. SAMTOOLS_FILTER was getting unsynchronised data from ch_reads and PACBIO_FILTER.out.list. The fix is to pair elements in those two channels before feeding SAMTOOLS_FILTER.

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• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
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[gq1]

Looks good for me.
But we need to fix the same problems in variantcalling pipeline.
sanger-tol/variantcalling#77

[gq1]

Merging to the main branch should be blocked by CI but not actually.
We should update the master branch to main in this CI:

readmapping/.github/workflows/branch.yml

Line 6 in a27e9ce

branches: [master]

[muffato]

Merging to the main branch should be blocked by CI but not actually. We should update the master branch to main in this CI:

readmapping/.github/workflows/branch.yml

Line 6 in a27e9ce

branches: [master]

Interesting find. I can see that the expected way is to name the branch patch.

I added a commit to this PR to fix master/main in .github/workflows/branch.yml