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[BUG FIX] Related to issue #207 on conda_local profile #208

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[BUG FIX] Related to issue #207 on conda_local profile #208

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6a83619
hot fix on conda_local_config
Mxrcon Jul 11, 2024
da98be1
Merge branch 'master' into patch-1
abhi18av Sep 5, 2024
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17 changes: 9 additions & 8 deletions conf/conda_local.config
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Original file line number Diff line number Diff line change
Expand Up @@ -19,25 +19,26 @@ process {
}


withName:
'TBPROFILER.*' {
withName:
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
//environment does exist:
conda = "${params.conda_envs_location}/magma-tbprofiler-env"
conda = "${params.conda_envs_location}/magma-env-1"

//environment does NOT exist: the env file contains all the info to create the environment "magma-env-1"
//conda = "${params.conda_envs_location}/magma-tbprofiler-env.yml"
//conda = "${params.conda_envs_location}/magma-env-1.yml"
}


withName:
'GATK.*|LOFREQ.*|DELLY.*|TBPROFILER.*|MULTIQC.*|FASTQC.*|UTILS.*|FASTQ.*|SAMPLESHEET.*' {
withName:
'TBPROFILER.*' {
//environment does exist:
conda = "${params.conda_envs_location}/magma-env-1"
conda = "${params.conda_envs_location}/magma-tbprofiler-env"

//environment does NOT exist: the env file contains all the info to create the environment "magma-env-1"
//conda = "${params.conda_envs_location}/magma-env-1.yml"
//conda = "${params.conda_envs_location}/magma-tbprofiler-env.yml"
}


withName:
'BWA.*|IQTREE.*|SNPDISTS.*|SNPSITES.*|BCFTOOLS.*|BGZIP.*|SAMTOOLS.*|SNPEFF.*|CLUSTERPICKER.*' {
//environment does exist:
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