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updated TrimGalore for multi-core support #65

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Merged
drpatelh merged 5 commits into from
Nov 21, 2019
Merged

updated TrimGalore for multi-core support #65

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bb42dee
updated TrimGalore for mult-core support
drewjbeh Nov 21, 2019
32c7afa
Update CHANGELOG.md
drewjbeh Nov 21, 2019
593233a
Update main.nf
drewjbeh Nov 21, 2019
fbdef55
Apply suggestions from code review
drewjbeh Nov 21, 2019
3b77b99
Update CHANGELOG.md
drewjbeh Nov 21, 2019
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.

### `Added`

* [#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!

### `Fixed`

* [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
Expand Down Expand Up @@ -36,6 +38,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
* Update homer `4.9.1` -> `4.10`
* Update bioconductor-deseq2 `1.20.0` -> `1.26.0`
* Update bioconductor-vsn `3.46.0` -> `3.54.0`
* Add pigz `2.3.4`

### `Deprecated`

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1 change: 1 addition & 0 deletions environment.yml
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Expand Up @@ -18,6 +18,7 @@ dependencies:
- conda-forge::r-lattice=0.20_38
- conda-forge::r-upsetr=1.4.0
- conda-forge::r-xfun=0.11
- conda-forge::pigz=2.3.4
- r::r-stringi=1.4.3

## bioconda packages
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6 changes: 3 additions & 3 deletions main.nf
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Expand Up @@ -526,7 +526,7 @@ if (params.skip_trimming) {
} else {
process TrimGalore {
tag "$name"
label 'process_long'
label 'process_medium'
publishDir "${params.outdir}/trim_galore", mode: 'copy',
saveAs: { filename ->
if (filename.endsWith(".html")) "fastqc/$filename"
Expand All @@ -553,13 +553,13 @@ if (params.skip_trimming) {
if (params.single_end) {
"""
[ ! -f ${name}.fastq.gz ] && ln -s $reads ${name}.fastq.gz
trim_galore --fastqc --gzip $c_r1 $tpc_r1 $nextseq ${name}.fastq.gz
trim_galore --cores $task.cpus --fastqc --gzip $c_r1 $tpc_r1 $nextseq ${name}.fastq.gz
"""
} else {
"""
[ ! -f ${name}_1.fastq.gz ] && ln -s ${reads[0]} ${name}_1.fastq.gz
[ ! -f ${name}_2.fastq.gz ] && ln -s ${reads[1]} ${name}_2.fastq.gz
trim_galore --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
trim_galore --cores $task.cpus --paired --fastqc --gzip $c_r1 $c_r2 $tpc_r1 $tpc_r2 $nextseq ${name}_1.fastq.gz ${name}_2.fastq.gz
"""
}
}
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