Resolve "process_align"

Alignment step using HiSat2

PR checklist

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

• Close issue
  Closes #4 (closed) Addresses alignData: add samtools to convert sam to bam and sort from #21 (closed)

/cc @ghenry @venkat.malladi /assign @ghenry

changed milestone to %v0.0.1

added Doing ~311 labels

marked as a Work In Progress

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• fa22c087...1c3a166b - 39 commits from branch develop
• 7c677cf1 - Merge develop into align branch

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@s181706

Will be checked in Consistency Checks

Units for align

• alignment count
• alignment file line count

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• bd3f9cb1 - Make metadata values inputs in downstream processes

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• 4c68aa57 - Updated references location to more universal location

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@s181706

To Do:

• put and set references in shared location
• make reference locations able to be set in configs
• reference = file ("/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/References/GRCh38.p12-S/hisat2") should be reference = Channel.fromPath("/project/BICF/BICF_Core/s181706/github/gudmap/rna-seq/References/GRCh38.p12-S/hisat2")

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• ebb7239c - Actually fixed references

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• f6c9944a - Reverted to ensure that Trim step is functional.

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• 25502c3d - Reverted to ensure that Trim step is functional.

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• d92d93f9 - Updated Hisat2 options, and output of parseMeta.

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• ca261a6b - Corrected scope-specific error in parseMeta.py

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• 19918779 - Manually specifying reference directory, need to automate. Also added...

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• 724ecd45 - Added indexing step to align, verified output files.

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• dda7cf97 - Added files necessary for CI of output files.

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• 88a757f3 - Added utils.py

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• 415fa462 - Added requested samtools flags for removing unmapped/double-mapped reads.

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• de4d2b8b - Updated test scripts.

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• 9afa2ee9 - Corrected CI file.

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• 60d6e158 - Corrected CI file.

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• 398747a6 - Update workflow/tests/test_alignReads.py

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• c1554d3c - Update .gitlab-ci.yml

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• a3564b7c - Update test_alignReads.py

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• dbdf865f - Update read comparison and decorator

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• 6b1e233a - Change single-end tests to reference correct experiment file.

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• e94986e1 - Fix the actual tests

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• 2333e8b4 - Remove line testing. As count_lines doesn't work for bam and bai files

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unmarked as a Work In Progress

assigned to @ghenry

changed the description

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• 2333e8b4...1a414a43 - 4 commits from branch develop
• fca8f872 - Merge branch 'develop' into 4-align

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• 3e44bbc0 - Add in change log to say that we made alignment files for user.

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changed the description

marked the checklist item README.md is updated as completed

marked the checklist item README.md is updated as incomplete

merged

mentioned in commit be3dd19b