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Metadata Sheet Discussion & Multilane merging

help wantedExtra attention is neededExtra attention is needed

questionFurther information is requestedFurther information is requested

Status: Closed (completed).

#209 In nf-core/eager;

· by apeltzer was closed on May 25, 2020

Fix --paired_end/--single_end behaviour

Status: Closed (completed).

#370 In nf-core/eager;

· by jfy133 was closed on Mar 19, 2020

Create parameters.settings.json file for CLI wizard

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#248 In nf-core/eager;

· by jfy133 was closed on Nov 6, 2020

Add BowTie2 support

enhancementNew feature or requestNew feature or request

feature

Status: Closed (completed).

#257 In nf-core/eager;

· by jfy133 was closed on Jun 23, 2020

Clean up code so more readable

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#320 In nf-core/eager;

· by jfy133 was closed on May 25, 2020

DeDup stats reporting is incorrect when unmapped reads included (the default in EAGER)

bugSomething isn't workingSomething isn't working

pendingAddressed on branch waiting for related PRAddressed on branch waiting for related PR

Status: Closed (completed).

#560 In nf-core/eager;

· by jfy133 was closed on Oct 13, 2020

Genotyping with pileupcaller produces genotypes for a single sample

Status: Closed (completed).

#457 In nf-core/eager;

· by TCLamnidis was closed on Jun 11, 2020

Discussion: Genotyping with pileupcaller

enhancementNew feature or requestNew feature or request

questionFurther information is requestedFurther information is requested

Status: Closed (completed).

#458 In nf-core/eager;

· by TCLamnidis was closed on Jul 13, 2020

Keep merged fastq from multiple lanes after AdapterRemoval

enhancementNew feature or requestNew feature or request

minor

Status: Closed (completed).

#454 In nf-core/eager;

· by paulayu was closed on Jun 14, 2020

Should contamination estimation be ran per library instead of per individual?

bugSomething isn't workingSomething isn't working

pendingAddressed on branch waiting for related PRAddressed on branch waiting for related PR

Status: Closed (completed).

#468 In nf-core/eager;

· by TCLamnidis was closed on Jul 12, 2020

Add output docs for all non-default modules.

documentation

Status: Closed (completed).

#475 In nf-core/eager;

· by jfy133 was closed on Jul 15, 2020

TSV Input: Add check a field is not empty

bugSomething isn't workingSomething isn't working

pendingAddressed on branch waiting for related PRAddressed on branch waiting for related PR

Status: Closed (completed).

#482 In nf-core/eager;

· by jfy133 was closed on Jul 12, 2020

Input FASTA check doesn't always work

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#479 In nf-core/eager;

· by jfy133 was closed on Jul 13, 2020

FastA indexing + bwa indexing

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#472 In nf-core/eager;

· by apeltzer was closed on Jun 30, 2020

Some more AWS issues

bugSomething isn't workingSomething isn't working

pendingAddressed on branch waiting for related PRAddressed on branch waiting for related PR

Status: Closed (completed).

#473 In nf-core/eager;

· by apeltzer was closed on Aug 3, 2020

Remove separation of PE/SE for deduplication

enhancementNew feature or requestNew feature or request

pendingAddressed on branch waiting for related PRAddressed on branch waiting for related PR

Status: Closed (completed).

#496 In nf-core/eager;

· by jfy133 was closed on Jul 15, 2020

DamageProfier exits 0 even if no output files

bugSomething isn't workingSomething isn't working

needs upstream fixNeeds a fix in the upstream tool projectNeeds a fix in the upstream tool project

Status: Closed (completed).

#434 In nf-core/eager;

· by jfy133 was closed on Jun 3, 2020

Add Proper AWS Test Data

documentation

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#418 In nf-core/eager;

· by apeltzer was closed on Jul 14, 2020

GLS Compatibility

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#404 In nf-core/eager;

· by lordkev was closed on Aug 3, 2020

Integrate MultiQC 1.9

Status: Closed (completed).

#419 In nf-core/eager;

· by jfy133 was closed on May 30, 2020

endorSpy sample names in MultiQC does not have name extensions removed

minor

Status: Closed (completed).

#420 In nf-core/eager;

· by jfy133 was closed on Jun 14, 2020

Unclear output doc figure for Samtools flagstat and add MALT/KRAKEN/MVA etc.

documentation

Status: Closed (completed).

#442 In nf-core/eager;

· by jfy133 was closed on Jul 15, 2020

Preserve realigned bam file when using gatk for genotyping

enhancementNew feature or requestNew feature or request

Status: Closed (completed).

#444 In nf-core/eager;

· by aidaanva was closed on Jul 13, 2020

Process tag warning using Nextflow 20.05.2

bugSomething isn't workingSomething isn't working

minor

Status: Closed (completed).

#439 In nf-core/eager;

· by aidaanva was closed on Jun 3, 2020

Add validation that if mapping quality changes needs filtering to be turned on

Status: Closed (completed).

#438 In nf-core/eager;

· by jfy133 was closed on Jun 9, 2020