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Hackathon March 2021
DSL2
Primary focus
Group members
New modules - Achievements
Update test files for all modules
New module sequenzautils/bam2seqz
New module sequenzautils/gcwiggle
New module cnvkit
New module picard/collectwgsmetrics
New module prokka
Update module shovill
New module vcftools
New module samtools/merge
New module samtools/fastq
New module strelka/germline
New module ucsc/bed12tobigbed
New module freebayes/single
New module fgbio/fastqtobam
New module adam/markduplicates
-u $(id -u):$(id -g)
specified indocker.runOptions
failing tests; see discussion on Slack and e.g. https://github.com/nf-core/tools/pull/351#issuecomment-581320133New module unicycler
New module: AdapterRemoval
New module: bismark/align
New module: bismark/report
New module: bismark/summary
New module: allelecounter
New module Kallisto/quant
New module: DamageProfiler
New module: prodigal [Gregor]
New module: gatk4/applybqsr
New module: gatk4/baserecalibrator
New module: gatk4/indexfeaturefile
new module: gatk4/fastqtosam
New module: gatk4/genotypegvcfs
New module: gatk4/markduplicates
New module: ensembl-VEP
New module: msisensor/scan
New module: msisensor/msi
New module: kb/ref
New module: kb/count
New module: NanoPlot
Modules Testing - Achievements
Human data set
Nanopore SARS-CoV2 test dataset
Changes to test data
Remove runOptions from docker profile
-u $(id -u):$(id -g)
for Docker in nf-coreOther - Achievements
Re-organised test data for different platforms
New test data config (@everyone!🎉)
Update CI tests to add linting and to bypass limit (Edmund)
Added more docs about local installation (properly tested modules has helped!)
Updated PR template to encourage linking the corresponding issues [#312 by Gregor]
Add docs for running tests locally with pytest [#338 by Harshil]
modules with custom scripts
${moduleDir}/bin/my_script.sh
works in principle but breaks the cache#tools
?