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Add changelog and fix for issue with index #221

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Jun 9, 2019
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Add changelog and fix for issue with index #221

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2f0621f
Add changelog and fix for issue with index
apeltzer Jun 9, 2019
2316ff0
Add collect - thanks @drpatelh
apeltzer Jun 9, 2019
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20 changes: 16 additions & 4 deletions CHANGELOG.md
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@@ -1,4 +1,5 @@
# nf-core/eager: Changelog

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
Expand All @@ -13,18 +14,19 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
/(https://github.com/nf-core/eager/issues/182)
* Merged in [nf-core/tools](https://github.com/nf-core/tools) release V1.6 template changes
* A lot more automated tests using Travis CI
* Don't ignore DamageProfiler errors anymore
* Don't ignore DamageProfiler errors anymore

### `Fixed`

* [#152](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
* [#176](https://github.com/nf-core/eager/pull/176) - Increase runtime for DamageProfiler on [large reference genomes](https://github.com/nf-core/eager/issues/173)
* [#172](https://github.com/nf-core/eager/pull/152) - DamageProfiler errors [won't crash entire pipeline anymore](https://github.com/nf-core/eager/issues/171)
* [#174](https://github.com/nf-core/eager/pull/190) - Publish DeDup files [properly](https://github.com/nf-core/eager/issues/183)
* [#196](https://github.com/nf-core/eager/pull/196) - Fix reference [issues](https://github.com/nf-core/eager/issues/150)
* [#196](https://github.com/nf-core/eager/pull/196) - Fix issues with PE data being mapped incompletely
* [#200](https://github.com/nf-core/eager/pull/200) - Fix minor issue with some [typos](https://github.com/nf-core/eager/pull/196)
* [#210](https://github.com/nf-core/eager/pull/210) - Fix PMDTools [encoding issue](https://github.com/pontussk/PMDtools/issues/6) from `samtools calmd` generated files by running through `samtools view` first

* [#210](https://github.com/nf-core/eager/pull/210) - Fix PMDTools [encoding issue](https://github.com/pontussk/PMDtools/issues/6) from `samtools calmd` generated files by running through `sa]mtools view` first
* [#221](https://github.com/nf-core/eager/pull/221) - Fix BWA Index [not being reused by multiple samples](https://github.com/nf-core/eager/issues/219)

### `Dependencies`

Expand All @@ -35,7 +37,6 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* Updated damageprofiler 0.4.4 -> 0.4.5
* Updated r-rmarkdown 1.11 -> 1.12


## [2.0.6] - 2019-03-05

### `Added`
Expand All @@ -51,28 +52,33 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* [#145](https://github.com/nf-core/eager/pull/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)

### `Dependencies`

* Picard Tools 2.18.23 -> 2.18.27
* GATK 4.0.12.0 -> 4.1.0.0
* FastP 0.19.6 -> 0.19.7

## [2.0.5] - 2019-01-28

### `Added`

* [#127](https://github.com/nf-core/eager/pull/127) - Added a second testcase for testing the pipeline properly
* [#129](https://github.com/nf-core/eager/pull/129) - Support BAM files as [input format](https://github.com/nf-core/eager/issues/41)
* [#131](https://github.com/nf-core/eager/pull/131) - Support different [reference genome file extensions](https://github.com/nf-core/eager/issues/130)

### `Fixed`

* [#128](https://github.com/nf-core/eager/issues/128) - Fixed reference genome handling errors

### `Dependencies`

* Picard Tools 2.18.21 -> 2.18.23
* R-Markdown 1.10 -> 1.11
* FastP 0.19.5 -> 0.19.6

## [2.0.4] - 2019-01-09

### `Added`

* [#111](https://github.com/nf-core/eager/pull/110) - Allow [Zipped FastA reference input](https://github.com/nf-core/eager/issues/91)
* [#113](https://github.com/nf-core/eager/pull/113) - All files are now staged via channels, which is considered best practice by Nextflow
* [#114](https://github.com/nf-core/eager/pull/113) - Add proper runtime defaults for multiple processes
Expand All @@ -87,27 +93,33 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
## [2.0.3] - 2018-12-12

### `Added`

* [#80](https://github.com/nf-core/eager/pull/80) - BWA Index file handling
* [#77](https://github.com/nf-core/eager/pull/77) - Lots of documentation updates by [@jfy133](https://github.com/jfy133)
* [#81](https://github.com/nf-core/eager/pull/81) - Renaming of certain BAM options
* [#92](https://github.com/nf-core/eager/issues/92) - Complete restructure of BAM options

### `Fixed`

* [#84](https://github.com/nf-core/eager/pull/85) - Fix for [Samtools index issues](https://github.com/nf-core/eager/issues/84)
* [#96](https://github.com/nf-core/eager/issues/96) - Fix for [MarkDuplicates issues](https://github.com/nf-core/eager/issues/96) found by [@nilesh-tawari](https://github.com/nilesh-tawari)

### Other

* Added Slack button to repository readme

## [2.0.2] - 2018-11-03

### `Changed`

* [#70](https://github.com/nf-core/eager/issues/70) - Uninitialized `readPaths` warning removed

### `Added`

* [#73](https://github.com/nf-core/eager/pull/73) - Travis CI Testing of Conda Environment added

### `Fixed`

* [#72](https://github.com/nf-core/eager/issues/72) - iconv Issue with R in conda environment

## [2.0.1] - 2018-11-02
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6 changes: 3 additions & 3 deletions main.nf
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Expand Up @@ -709,7 +709,7 @@ process bwa {

input:
set val(name), file(reads) from ch_clipped_reads.mix(ch_read_files_converted_mapping_bwa)
file index from bwa_index
file index from bwa_index.collect()


output:
Expand Down Expand Up @@ -776,7 +776,7 @@ process circularmapper{

input:
set val(name), file(reads) from ch_clipped_reads_circularmapper.mix(ch_read_files_converted_mapping_cm)
file index from ch_circularmapper_indices
file index from ch_circularmapper_indices.collect()
file fasta from fasta_for_indexing

output:
Expand Down Expand Up @@ -821,7 +821,7 @@ process bwamem {

input:
set val(name), file(reads) from ch_clipped_reads_bwamem.mix(ch_read_files_converted_mapping_bwamem)
file index from bwa_index_bwamem
file index from bwa_index_bwamem.collect()

output:
file "*.sorted.bam" into ch_bwamem_mapped_reads_idxstats,ch_bwamem_mapped_reads_filter,ch_bwamem_mapped_reads_preseq, ch_bwamem_mapped_reads_damageprofiler, ch_bwamem_mapped_reads_strip
Expand Down