Resolve "samtools sort: couldn't allocate memory for bam_mem"

Fixes some newly discovered metadata errors.
Has been tested with --upload false
Testing overnight (with `--upload true --server dev

• W-RCGG: submitted stranded/spike = blank & have fastq's not matching convention
• 14-3R4R: submitted stranded/spike = unspecified
• Q-Y5HT: fastq structure error (fastq+bam concatenation)
• W-RB84: no errors

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!
• [ ] Documentation in docs is updated
• Replace dag.png with the most recent CI pipeline integrated_pe artifact
• [ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
• [ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
• CHANGELOG.md is updated
• [ ] README.md is updated
• [ ] LICENSE.md is updated with new contributors
• [ ] Docker images moved to production release and changed in pipeline
• [ ] Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #105 (closed) Closes #106 (closed) Closes #107 (closed) Closes #108 (closed) Closes #109 (closed)

/cc @ghenry @venkat.malladi

changed milestone to %v2.0.0

added Doing bug critical labels

added 2 commits

• f453a4e3 - Fix no fastq's present in inputBag
• 957b7679 - Fix no fastq error detail

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added 3 commits

• 94dac4ed - Add premature fail execution run upload with fastq file error
• 8f5efffa - Remove ends manual from parse metadata unit ci
• e1819c40 - Add excape to bracket in echo

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added 2 commits

• f83a3d8c - Add unexpected meta and fastq structure error ci integration tests
• ded8b61b - Add back ends manual to ci unit for parse, but manual

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added 1 commit

• c36fec03 - Add back ends manual to parse ci unit

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added 1 commit

• 985cef31 - Fix fastqc error detection

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added 2 commits

• e7c65fea - Catch error if fastq file error grep
• 9e121dac - Make sampled align use > 32GB nodes on BioHPC

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changed the description

added 1 commit

• 1fe7d8b3 - Use 1 less process for samtools threading and limit memto 75% of available

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added 1 commit

• e1d95064 - Update DAG

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

marked this merge request as ready

approved this merge request

enabled an automatic merge when the pipeline for e1d95064 succeeds

mentioned in commit 474a1d3e

merged