eager

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New module: calmd

3

#778 lists samtools calmd as needing DSL2 module creation.

JackCurragh

- DEDUP/MARKDUPLICATES - MTNUCRATIO - NUCLEARCONTAMINATION (HUMAN) - SEXDETERRMINE - PMDTOOLS - BAMUTILS - MAPDAMAGE2 (RESCALE) - GATKUNIFIEDGENOTYPER - GATKHAPLOTYPECALLER - PILEUPCALLER - FREEBAYES - ANGSD ## NEW - Dedup...

jfy133

DSL2: metagenomics

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- BBDUK - HOSTREMOVAL - MALT/KRAKEN - MALTEXTRACT - KRAKENPARSE ## New - Option: mapped OR unmapped reads to metagenomic screeming - KRAKENUNIQ - METAPHLAN3 - PRINSEQ (alternative complexity filterer)

jfy133

DSL2: stats

1

- FLAGSTAT - ENDORSPY - BEDTOOLS - DAMAGEPROFILER - QUALIMAP - VCF2GENOME - MULTIVCFANALYZER - BCFTOOLS ## New - SNPEFF(?) ```[tasklist] ### Tasks - [ ] https://github.com/nf-core/eager/issues/1002 - [ ]...

jfy133

Mitochondrial and Ych haplotype callers

7

SalWas1

- [ ] Update all citations - [ ] Update README citations - [ ] Update README list of tools - [ ] Update workflow diagrams (with version number) -...

jfy133

DSL2: replaces input_check with fromSamplesheet (nf-validation)

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closes #1012 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

jfy133

DSL2: Convert input BAM

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Closes #987 ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

TCLamnidis

DSL2: metagenomics

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TODOS: - [ ] Ensure files passed to metagenomics profiling are identifiable with outputted names (eg should be able to distinguish mapped, vs unmapped to ref (if user selects 'all':...

ilight1542

CRAM output

1

It would be nice to either swap to CRAM files, or offer that as an option.

TCLamnidis