diff --git a/nextflow.config b/nextflow.config index 19617f7..ac4a314 100755 --- a/nextflow.config +++ b/nextflow.config @@ -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 = "${projectDir}/multiqc" -/* - * defines execution profiles for different environments - */ +/* + * defines execution profiles for different environments + */ profiles { standard { @@ -66,15 +66,21 @@ profiles { 'conda' { conda.enabled = true - conda.channels = 'seqera,conda-forge,bioconda,defaults' + conda.channels = 'conda-forge,bioconda,defaults' } - + + 'mamba' { + conda.enabled = true + conda.useMicromamba = true + conda.channels = 'conda-forge,bioconda,defaults' + } + 'slurm' { process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0' process.executor = 'slurm' singularity.enabled = true } - + 'batch' { params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq' params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa' @@ -90,7 +96,7 @@ profiles { process.container = 'docker.io/nextflow/rnaseq-nf:v1.3.0' params.reads = 's3://rnaseq-nf/data/ggal/lung_{1,2}.fq' params.transcriptome = 's3://rnaseq-nf/data/ggal/transcript.fa' - } + } 'google-batch' { params.transcriptome = 'gs://rnaseq-nf/data/ggal/transcript.fa' @@ -117,7 +123,7 @@ profiles { azure { batch { location = 'westeurope' - accountName = "$AZURE_BATCH_ACCOUNT_NAME" + accountName = "$AZURE_BATCH_ACCOUNT_NAME" accountKey = "$AZURE_BATCH_ACCOUNT_KEY" autoPoolMode = true deletePoolsOnCompletion = true