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Add -profile mamba #28

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Oct 23, 2024
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Add -profile mamba #28

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32 changes: 19 additions & 13 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -9,25 +9,25 @@
* defined by the Mozilla Public License, v. 2.0.
*
*/

manifest {
description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
description = 'Proof of concept of a RNA-seq pipeline implemented with Nextflow'
author = 'Paolo Di Tommaso'
nextflowVersion = '>=23.10.0'
}

/*
* default params
/*
* default params
*/

params.outdir = "results"
params.reads = "${projectDir}/data/ggal/ggal_gut_{1,2}.fq"
params.transcriptome = "${projectDir}/data/ggal/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
params.multiqc = "${projectDir}/multiqc"

/*
* defines execution profiles for different environments
*/
/*
* defines execution profiles for different environments
*/

profiles {
standard {
Expand Down Expand Up @@ -66,15 +66,21 @@ profiles {

'conda' {
conda.enabled = true
conda.channels = 'seqera,conda-forge,bioconda,defaults'
conda.channels = 'conda-forge,bioconda,defaults'
}


'mamba' {
conda.enabled = true
conda.useMicromamba = true
conda.channels = 'conda-forge,bioconda,defaults'
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worth to remove defaults?

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oops! Definitely, that was a mistake on my part sorry.

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#29

}

'slurm' {
process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
process.executor = 'slurm'
singularity.enabled = true
}

'batch' {
params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
Expand All @@ -90,7 +96,7 @@ profiles {
process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0'
params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq'
params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa'
}
}

'google-batch' {
params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa'
Expand All @@ -117,7 +123,7 @@ profiles {
azure {
batch {
location = 'westeurope'
accountName = "$AZURE_BATCH_ACCOUNT_NAME"
accountName = "$AZURE_BATCH_ACCOUNT_NAME"
accountKey = "$AZURE_BATCH_ACCOUNT_KEY"
autoPoolMode = true
deletePoolsOnCompletion = true
Expand Down
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