Resolve "process_count"

Add featureCounts (including manual TPM calculation in R: decided not to calculate FPKM because they are essentially the same thing, and since Data-Hub requested TPM, that's what was calulated)

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!
• Replace dag.png with the most recent CI pipleine integrated_pe artifact

• Close issue
  Closes #56 (closed)

/cc @ghenry @venkat.malladi

changed milestone to %v0.0.1

added Doing discussion labels

marked the checklist item This comment contains a description of changes (with reason) as completed

marked the checklist item If you've fixed a bug or added code that should be tested, add tests! as completed

marked the checklist item Replace dag.png with the most recent CI pipleine integrated_pe artifact as completed

marked the checklist item *Close issue* as completed

added 1 commit

• 2c5bbdc1 - Fix exit for tests in calculateTPM.R

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marked as a Work In Progress

changed the description

added 1 commit

• 387290a1 - Added paired end and stranded features to featureCounts.

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added 1 commit

• 3f71105b - Fix spelling errors

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marked the checklist item Replace dag.png with the most recent CI pipleine integrated_pe artifact as incomplete

marked the checklist item *Close issue* as incomplete

unmarked as a Work In Progress

added 1 commit

• 3c9c7d4d - Changed tag from 'gene_id' to 'gene_name'

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added 43 commits

• 3c9c7d4d...ad35f8df - 42 commits from branch develop
• 03aa79a9 - Merge resolution

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added 1 commit

• 1e445926 - Improved logging and removal of redundant variables.

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added 1 commit

• 810cfffb - Changed executor to local for inferMetaData to attempt to run quicker.

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added 1 commit

• 47e9c3e6 - Reverted to using SLURM with super queue.

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added 1 commit

• 28f1a97f - Code review changes/corrections

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added 1 commit

• 7d2108a5 - Corrected typo in makeFeatureCounts test.

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added 1 commit

• 5acdbca8 - Updated exit message.

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resolved all discussions

marked the checklist item *Close issue* as completed

marked the checklist item Replace dag.png with the most recent CI pipleine integrated_pe artifact as completed

enabled an automatic merge when the pipeline for 5acdbca8 succeeds

merged

mentioned in commit fe73c982