Merge pull request #984 from nf-core/seqinspector_ABH

Added seqinspector/hasta.config

Author: maxulysse

conf/pipeline/seqinspector/hasta.config

@@ -0,0 +1,72 @@
+process {
+
+
+    // TODO nf-core: Check the defaults for all processes
+    cpus   = { 1      * task.attempt }
+    memory = { 6.GB   * task.attempt }
+    time   = { 4.h    * task.attempt }
+
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 2
+    maxErrors     = '-1'
+
+
+    // Subsampling reads
+    withName: 'SEQTK_SAMPLE' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    // Quality control
+    withName: 'FASTQC' {
+        cpus = 2
+        memory = { 36.GB * task.attempt }
+        time = { 8.h * task.attempt }
+    }
+    withName: 'SEQFU_STATS' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    withName: 'FASTQSCREEN_FASTQSCREEN' {
+        cpus = 6
+        memory = { 36.GB * task.attempt }
+        time = { 8.h * task.attempt }
+    }
+
+    // Reference genome processing
+    withName: 'BWAMEM2_INDEX' {
+        cpus = 12
+        memory = { 72.GB * task.attempt }
+        time = { 16.h * task.attempt }
+    }
+    withName: 'BWAMEM2_MEM' {
+        cpus = 6
+        memory = { 35.GB * task.attempt }
+        time = { 16.h * task.attempt }
+    }
+    withName: 'SAMTOOLS_INDEX' {
+        cpus = 6
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    withName: 'SAMTOOLS_FAIDX' {
+        cpus = 6
+        memory = { 6.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+    // Picard metrics
+    withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
+        cpus = 4
+        memory = { 8.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+
+    // MultiQC aggregation
+    withName: 'MULTIQC_GLOBAL|MULTIQC_PER_TAG' {
+        cpus = 4
+        memory = { 4.GB * task.attempt }
+        time = { 4.h * task.attempt }
+    }
+}