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Implement sample merging#1026

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Donaim wants to merge 11 commits intomastercfe-lab/MiCall:masterfrom merge_samplescfe-lab/MiCall:merge_samplesCopy head branch name to clipboard

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Commits on Feb 14, 2024

• Make bad_cycles.csv argument optional in trim_fastqs.py

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• Add merge_samples command to micall_docker.py

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• Factor merge_fastqs from micall_docker.py into a separate script

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• Add Singularity entry for the new merge_fastqs pipeline

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• Fix input arguments to merge_fastqs in Singularity file

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• Add more tests for merge_fastqs.py script

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• Ensure that output directories exist in merge_fastqs.py

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• Fix typo in merge_fastqs.py

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• Compress final outputs in merge_samples when --unzip is not used

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Commits on Feb 16, 2024

• Merge fastqs: support arbitrary number of inputs

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• Merge fastqs: add documentation

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