Merge pull request #373 from genomic-medicine-sweden/taxprofiler_hasta

Add hasta config for taxprofiler

README.md

@@ -201,6 +201,7 @@ Currently documentation is available for the following pipelines within specific
   - [UPPMAX](docs/pipeline/sarek/uppmax.md)
 - taxprofiler
   - [EVA](docs/pipeline/taxprofiler/eva.md)
+  - [hasta](docs/pipeline/taxprofiler/hasta.md)
 
 ### Pipeline-specific documentation
 

conf/pipeline/taxprofiler/hasta.config

@@ -0,0 +1,16 @@
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Sofia Stamouli (@sofstam)'
+  config_profile_description = 'nf-core/taxprofiler HASTA profile provided by nf-core/configs'
+}
+
+process {
+
+    withName:'BBMAP_BBDUK' {
+        memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
+    }
+
+    withName: 'MALT_RUN' {
+        memory = { check_max( 80.GB   * task.attempt, 'memory' ) }
+    }
+}

docs/pipeline/taxprofiler/hasta.md

@@ -0,0 +1,19 @@
+# nf-core/configs: eva taxprofiler specific configuration
+
+Extra specific configuration for taxprofiler pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile hasta`.
+
+This will download and launch the taxprofiler specific [`hasta.config`](../../../conf/pipeline/taxprofiler/hasta.config) which has been pre-configured with a setup suitable for the hasta cluster.
+
+Example: `nextflow run nf-core/taxprofiler -profile hasta`
+
+## taxprofiler specific configurations for hasta
+
+Specific configurations for hasta has been made for taxprofiler.
+
+### General profiles
+
+- The general hasta profile runs with default nf-core/taxprofiler parameters, but with modifications to account for issues with: BBDUK and MALT.

pipeline/taxprofiler.config

@@ -1,3 +1,14 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/taxprofiler custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/taxprofiler folder and imported
+ * under a profile name here.
+ */
+
 profiles {
+  hasta { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/hasta.config" }
   eva { includeConfig "${params.custom_config_base}/conf/pipeline/taxprofiler/eva.config" }
 }