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iGenomes fix #123

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merged 3 commits into from
Nov 26, 2019
Merged

iGenomes fix #123

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7ca82c4
Move reference params back into main.nf
ewels Nov 25, 2019
c76200b
Changelog, drop memory for trim_galore
ewels Nov 25, 2019
fbd3812
Add Python 3.7 as a dependency for conda environment
ewels Nov 26, 2019
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,7 @@
### New features

* Added multicore support for `TrimGalore!`
* Improved the multicore support for Bismark methXtract for more parallelisation ([#121](https://github.com/nf-core/methylseq/issues/121))

### Software updates

Expand All @@ -15,6 +16,7 @@

### Pipeline Updates

* Fixed bug where the iGenomes config was loaded after the references were set ([#121](https://github.com/nf-core/methylseq/issues/121))
* Removed awsbatch config profile because it is now served by [nf-core/configs](https://github.com/nf-core/configs)

## [v1.4](https://github.com/nf-core/methylseq/releases/tag/1.4) - 2019-11-19
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2 changes: 1 addition & 1 deletion conf/base.config
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Expand Up @@ -28,7 +28,7 @@ process {
}
withName:trim_galore {
cpus = { check_max( 15 * task.attempt, 'cpus') }
memory = { check_max( 16.GB * task.attempt, 'memory') }
memory = { check_max( 6.GB * task.attempt, 'memory') }
time = { check_max( 1.d * task.attempt, 'time') }
}
withName:bismark_align {
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1 change: 1 addition & 0 deletions environment.yml
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Expand Up @@ -6,6 +6,7 @@ channels:
- bioconda
- defaults
dependencies:
- python=3.7
- conda-forge::pigz=2.3.4
- conda-forge::r-markdown=1.1
- bioconda::fastqc=0.11.8
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6 changes: 6 additions & 0 deletions main.nf
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Expand Up @@ -94,6 +94,12 @@ assert params.aligner == 'bwameth' || params.aligner == 'bismark' || params.alig
* SET UP CONFIGURATION VARIABLES
*/

// These params need to be set late, after the iGenomes config is loaded
bismark_index = params.genome ? params.genomes[ params.genome ].bismark ?: false : false
bwa_meth_index = params.genome ? params.genomes[ params.genome ].bwa_meth ?: false : false
fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
fasta_index = params.genome ? params.genomes[ params.genome ].fasta_index ?: false : false

// Check if genome exists in the config file
if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}"
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4 changes: 0 additions & 4 deletions nextflow.config
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Expand Up @@ -13,10 +13,6 @@ params {
reads = "data/*_R{1,2}.fastq.gz"
single_end = false
aligner = 'bismark'
bismark_index = params.genome ? params.genomes[ params.genome ].bismark ?: false : false
bwa_meth_index = params.genome ? params.genomes[ params.genome ].bwa_meth ?: false : false
fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
fasta_index = params.genome ? params.genomes[ params.genome ].fasta_index ?: false : false
comprehensive = false
ignore_flags = false
meth_cutoff = false
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