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| process { | ||
| withName: PARABRICKS_FQ2BAMMETH { | ||
| cache = 'lenient' // This is set because in the module command the index files are touched so as to have bwameth not complain | ||
| ext.args = '--low-memory' |
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we don't need this in all the runs, just on the tests
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| } | ||
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| // SAMTOOLS_INDEX after PICARD_MARKDUPLICATES - publish to deduplicated when deduplication runs |
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we don't need this since we publish the *markdup.sorted.bam and .bai
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@nf-core-bot fix linting |
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@nf-core-bot fix linting |
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The linting really is giving me a hard time lol |
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Tests 2 for conda, singularity and docker show different snapshots for the 'latest' version vs the 25.04, unsure why. |
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).