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Fix for post-dup steps #151

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Merged
apeltzer merged 7 commits into from
Feb 27, 2019
Merged

Fix for post-dup steps #151

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7405c8e
Fix for post-dup steps
apeltzer Feb 25, 2019
7e4035d
Nicer changelog [skip ci]
apeltzer Feb 25, 2019
76e0cbd
Its unpublished stuff [skip ci]
apeltzer Feb 25, 2019
0fb1481
Merge branch 'dev' into fix-post-dedup-steps
apeltzer Feb 26, 2019
fabd1a3
Should fix the remaining issues
apeltzer Feb 26, 2019
24ea4b7
Merge branch 'fix-post-dedup-steps' of https://github.com/apeltzer/ea…
apeltzer Feb 26, 2019
c69261d
Address issues with qualimap / multiqc / multiple samples and reporting
apeltzer Feb 26, 2019
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6 changes: 3 additions & 3 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

## [Unpublished / Dev Branch]

### `Added`

### `Fixed`
* [#145](https://github.com/nf-core/eager/pull/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)
* [#151](https://github.com/nf-core/eager/pull/151) - Fixed [post-deduplication step errors](https://github.com/nf-core/eager/issues/128
* [#147](https://github.com/nf-core/eager/pull/147) - Fix Samtools Index for [large references](https://github.com/nf-core/eager/issues/146)
* [#145](https://github.com/nf-core/eager/pull/145) - Added Picard Memory Handling [fix](https://github.com/nf-core/eager/issues/144)

## [2.0.5] - 2019-01-28

Expand All @@ -21,6 +20,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

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

### `Dependencies`
* Picard Tools 2.18.21 -> 2.18.23
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10 changes: 5 additions & 5 deletions main.nf
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Expand Up @@ -907,7 +907,7 @@ process damageprofiler {

input:
file bam from ch_mapped_reads_damageprofiler.mix(ch_mapped_reads_damageprofiler_cm,ch_bwamem_mapped_reads_damageprofiler)
file fasta from ch_fasta_for_damageprofiler
file fasta from ch_fasta_for_damageprofiler.first()
file bai from ch_bam_index_for_damageprofiler


Expand All @@ -934,7 +934,7 @@ process qualimap {

input:
file bam from ch_bam_filtered_qualimap
file fasta from ch_fasta_for_qualimap
file fasta from ch_fasta_for_qualimap.first()

output:
file "*" into ch_qualimap_results
Expand Down Expand Up @@ -1140,12 +1140,12 @@ process multiqc {
file multiqc_config from ch_multiqc_config.collect().ifEmpty([])
file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([])
file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
file ('software_versions/*') from software_versions_yaml.collect().ifEmpty([])
file ('software_versions/software_versions_mqc*') from software_versions_yaml.collect().ifEmpty([])
file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([])
file ('idxstats/*') from ch_idxstats_for_multiqc.collect().ifEmpty([])
file ('preseq/*') from ch_preseq_results.collect().ifEmpty([])
file ('damageprofiler/*') from ch_damageprofiler_results.collect().ifEmpty([])
file ('qualimap/*') from ch_qualimap_results.collect().ifEmpty([])
file ('damageprofiler/dmgprof*/*') from ch_damageprofiler_results.collect().ifEmpty([])
file ('qualimap/qualimap*/*') from ch_qualimap_results.collect().ifEmpty([])
file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([])
file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([])
file ('fastp/*') from ch_fastp_for_multiqc.collect().ifEmpty([])
Expand Down
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