nf-core bump-version . 2.5.1 fix script name in docs fix markdownlint fix autoMounts in singularity profile, closes nf-core#48 add patch to branch protection use correct tag for containers close nf-core#49 update CHANGELOG Try to fix branch protection Update README.md reducing CPU usage for Mpileup cleanup with meld some docs additions Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> added extra space Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> Update docs/downstream.md Co-Authored-By: Maxime Garcia <maxime.garcia@scilifelab.se> First time CF is working with extra pileups First working version Removing nf-core#51 and moving downstream to szilvajuhos/btb-scripts Fixing some null parameters and C&P typos yet an other version that somehow worked remove --normal_pileup and --tumor_pileup params update freebayes germline command update changelog fix --save_bam_mapped + small typos update CHANGELOG add step controlfreec use nf-core header update config cleanup add mappability files to igenomes better name for tsv file fix output directory enable usage of - in names of tools or steps better default for coefficientofvariation improve help update and reorder params reorder and update params update and reorder params update docs fix prepare_recalibration step update CHANGELOG Apply suggestions from code review

Release 2.5 pulls dev SNPEff Containers #49

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Release 2.5 pulls `dev` SNPEff Containers #49