Pseudo PR for Pipeline Review #49

Closed

apeltzer wants to merge 196 commits intoempty_devfrom

Commits on Mar 15, 2018

Added Git Ignore files as well :-)
Alexander Peltzer
committed

Commits on Jun 3, 2018

Multiple adjustments to follow nf-core guidelines
Alexander Peltzer
committed
Added Gitter badge
Alexander Peltzer
committed
Readme + Language type adjustment
Alexander Peltzer
committed
Updated environment yml
Alexander Peltzer
committed
EAGER2.0ified pipeline
Alexander Peltzer
committed
Added software version scraping on NXF level
Alexander Peltzer
committed
Add info for future steps
Alexander Peltzer
committed
Add DamageProfiler to env
Alexander Peltzer
committed
Added parameter documentation for later
Alexander Peltzer
committed
Basic clipping with Clip & Merge
Alexander Peltzer
committed
Add reverse and forward adaptors for C&M
Alexander Peltzer
committed
Basic clip & merging modules
Alexander Peltzer
committed
Prefixes missing in AR
Alexander Peltzer
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Not mostly
Alexander Peltzer
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Adding logos and README update
Alexander Peltzer
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More cosmetics
Alexander Peltzer
committed
Added WIP disclaimer
Alexander Peltzer
committed
SequenceTools missing too
Alexander Peltzer
committed
Update Dockerfile
apeltzer
authored
Readme adjustments
Alexander Peltzer
committed
Merge pull request #7 from apeltzer/master
apeltzer
authored
Added config files for Tuebingen infrastructure, local singularity and docker testing
Alexander Peltzer
committed
Merge pull request #8 from apeltzer/master
apeltzer
authored
Gitattributes for config
Alexander Peltzer
committed
Cleaned config files and base config
Alexander Peltzer
committed
Merge pull request #9 from apeltzer/master
apeltzer
authored
Updated James' contact information
jfy133
authored
Merge pull request #12 from jfy133/patch-1
apeltzer
authored

Commits on Jun 12, 2018

change nf-EAGER to nf-core/EAGER2
maxulysse
committed
Merge pull request #16 from MaxUlysse/master
apeltzer
authored
Add better tests
Alexander Peltzer
committed
Add Singularity file
Alexander Peltzer
committed
removed old config files
Alexander Peltzer
committed
Added proper test profile
Alexander Peltzer
committed
Added Badge for Singularity hub
Alexander Peltzer
committed
Updated Badge for NXF 0.30.1
Alexander Peltzer
committed

Commits on Jun 14, 2018

Fixed linting tests, add pmdtools recipe
Alexander Peltzer
committed

Commits on Jun 21, 2018

Test with most current NXF version too
Alexander Peltzer
committed
Delete old run_test.sh script
Alexander Peltzer
committed
Fixing dockerfile
Alexander Peltzer
committed
Removed unrequired iGenomes paths
Alexander Peltzer
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Commits on Jul 4, 2018

Feature
Alexander Peltzer
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Feature
Alexander Peltzer
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Feature
Alexander Peltzer
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Feature
Alexander Peltzer
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Fix
Alexander Peltzer
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Commits on Jul 11, 2018

Add Add Stephen as collaborator
Alexander Peltzer
committed
Fix Use Https for markdown to html script
Alexander Peltzer
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Fix Move helpmessage down the road
Alexander Peltzer
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Fix Replace $ with withName: format fixing #18
Alexander Peltzer
committed

Commits on Aug 23, 2018

Update LICENSE
apeltzer
authored
Remove singularity, long live docker cloud
Alexander Peltzer
committed
Merge branch 'master' of https://github.com/nf-core/EAGER2
Alexander Peltzer
committed
eager2->eager
Alexander Peltzer
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Optimizing test profile
Alexander Peltzer
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Test profiles
Alexander Peltzer
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Follow new convention in testing
Alexander Peltzer
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Add params.readPaths
Alexander Peltzer
committed
This is paired end data
Alexander Peltzer
committed
Cleaning up for now
Alexander Peltzer
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Add initialization to genome variables
Alexander Peltzer
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Revert back to current syntax
Alexander Peltzer
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Add AWSBatch configuration possibilities
Alexander Peltzer
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Adapt travis tests
Alexander Peltzer
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indentation missing
Alexander Peltzer
committed
docs fixes
Alexander Peltzer
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Remove workflow oncomplete for now
Alexander Peltzer
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Remove try catch
Alexander Peltzer
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AWSBatch sanity checking
Alexander Peltzer
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Update Dockerfile
apeltzer
authored
Update environment.yml
apeltzer
authored
Tests should pass with this (they do locally)
Alexander Peltzer
committed

Commits on Aug 24, 2018

Fixing linting errors
Alexander Peltzer
committed
Update travis
Alexander Peltzer
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Adding manifest to nextflow config
Alexander Peltzer
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Adding pipelineversion
Alexander Peltzer
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Fixing remaining linting issues
Alexander Peltzer
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Update Dockerfile
apeltzer
authored
Update environment.yml
apeltzer
authored
Having custom set as default
Alexander Peltzer
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Remove genomes for now
Alexander Peltzer
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Add dump possibility for input debugging
Alexander Peltzer
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Add AdapterRemoval2 functionality
Alexander Peltzer
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Add AdapterRemovalFixPrefix
Alexander Peltzer
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AR improvements - missing only SE handling
Alexander Peltzer
committed

Commits on Oct 5, 2018

Initial template commit
Alexander Peltzer
committed
Merging everything with TEMPLATE Branch
Alexander Peltzer
committed
Fixing nextflow config
Alexander Peltzer
committed
Minor config fixes
Alexander Peltzer
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Minor fixes in config file
Alexander Peltzer
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Remove remaining merge conflicts
Alexander Peltzer
committed
Revert back old paths
Alexander Peltzer
committed
Fixed templates
Alexander Peltzer
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Fixing readme and config merge conflicts
Alexander Peltzer
committed
Bumping software versions
Alexander Peltzer
committed
EOF
Alexander Peltzer
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Fix for tests
Alexander Peltzer
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Fixing typo thanks to paolo
Alexander Peltzer
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Add SE handling for AdapterRemoval
Alexander Peltzer
committed
BWA mapping runs through well
Alexander Peltzer
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Add Samtools sort to BWA call
Alexander Peltzer
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Add Samtools idxstats
Alexander Peltzer
committed
Fixing running time for BWA
Alexander Peltzer
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Add Samtools filtering of BAMs
Alexander Peltzer
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Add preseq to environment
Alexander Peltzer
committed
This should work once the container is there
Alexander Peltzer
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Add possibility to have compressed fastq for unmapped reads failing to map
Alexander Peltzer
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Base config for preseq instability
Alexander Peltzer
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Adding defaults for skipping parameters
Alexander Peltzer
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Working damageprofiler
Alexander Peltzer
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Commits on Oct 6, 2018

Add qualimap to eager2
Alexander Peltzer
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Adding in DeDup + MarkDuplicates
Alexander Peltzer
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Adding in DeDup and MarkDuplicates
Alexander Peltzer
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More details about utilized tools in the pipeline
Alexander Peltzer
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MOre versions in report
Alexander Peltzer
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Commits on Oct 10, 2018

Merge branch 'master' into dev
apeltzer
authored
Merge pull request #28 from nf-core/dev
apeltzer
authored
Update issue templates
apeltzer
committed
Update issue templates
apeltzer
committed
Add fastp to environment yaml
Alexander Peltzer
committed
Add environment yaml
Alexander Peltzer
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Adding in complexity filtering, adressind issue #13
Alexander Peltzer
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Bump versions of fastqc and picard
Alexander Peltzer
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Adding in versions of bamUtil and fastp to report
Alexander Peltzer
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Typo fix
Alexander Peltzer
committed
Dependent channels, yeah :-)
Alexander Peltzer
committed
Proper script calls
Alexander Peltzer
committed
polyG filtering
Alexander Peltzer
committed
Adding in FastP
Alexander Peltzer
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Typos fixed
Alexander Peltzer
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Add bugfixing for software versions in report table
Alexander Peltzer
committed
Typo fix
Alexander Peltzer
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Fixing remaining software_versions collection issues
Alexander Peltzer
committed
Merge pull request #32 from nf-core/dev
apeltzer
authored
Working fastp examples
Alexander Peltzer
committed
Fixing SE read handling
Alexander Peltzer
committed
Fix remaining warnings
Alexander Peltzer
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Add multiple tests for SE, complexity filtering etc pp
Alexander Peltzer
committed
Merge pull request #33 from nf-core/master
apeltzer
authored
Merge pull request #34 from nf-core/dev
apeltzer
authored
Add DeDup histogram possibilities fixing #35
Alexander Peltzer
committed
Merge branch 'dev' of https://github.com/nf-core/eager into dev
Alexander Peltzer
committed
Add ideas to downstream processing
Alexander Peltzer
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Add idea of swabian names to name releases
Alexander Peltzer
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Add FastQC twice for checking after clipping/merging
Alexander Peltzer
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Add Mixin channel for file handling prior to pmdtools
Alexander Peltzer
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Add PMDtools skipping option
Alexander Peltzer
committed
PMDtools will work, but needs upstream fix
Alexander Peltzer
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Commits on Oct 12, 2018

Commits on Oct 15, 2018

Commits on Oct 17, 2018

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