Merge pull request #330 from nf-core/master

Pulling master to branch

.github/workflows/linting.yml

@@ -7,9 +7,7 @@ jobs:
     runs-on: ubuntu-18.04
     steps:
       - uses: actions/checkout@v1
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2
-        with:
-          node-version: '10'
       - name: Install markdownlint
         run: |
           npm install -g markdownlint-cli

conf/cbe.config

@@ -7,11 +7,9 @@ params {
 
 process {
   executor = 'slurm'
-  queue = { task.memory <= 170.GB ? 'c' : 'm' }
+  queue = { task.memory <= 120.GB ? 'c' : 'm' }
-  module = 'anaconda3/2019.10'
+  module = ['build-env/.f2021', 'build-env/f2021', 'anaconda3/2021.11']
-  
+  clusterOptions = { ( task.queue == 'g' ? '--gres gpu:1 ' : '' ) << ( (task.queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
-  // --signal option will be handled by nextflow after 21.10.0 release (see https://github.com/nextflow-io/nextflow/issues/2163)
-  clusterOptions = { '--signal B:USR2 ' << ( (queue == 'c' & task.time <= 1.h) ? '--qos rapid' : ( task.time <= 8.h ? '--qos short': ( task.time <= 48.h ? '--qos medium' : '--qos long' ) ) ) }
 }
 
 singularity {

conf/eva.config

@@ -30,7 +30,7 @@ profiles {
         config_profile_description = 'MPI-EVA archgen profile, provided by nf-core/configs.'
         max_memory = 256.GB
         max_cpus = 32
-        max_time = 720.h
+        max_time = 365.d
         //Illumina iGenomes reference file path
       }
 

conf/pipeline/eager/eva.config

@@ -19,57 +19,60 @@ process {
   withLabel:'sc_tiny'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 1.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'sc_small'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'sc_medium'{
     cpus = { check_max( 1, 'cpus' ) }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'mc_small'{
     cpus = { check_max( 2, 'cpus' ) }
     memory = { check_max( 4.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'mc_medium' {
     cpus = { check_max( 4, 'cpus' ) }
     memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-    time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'mc_large'{
      cpus = { check_max( 8, 'cpus' ) }
      memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-     time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
   }
 
   withLabel:'mc_huge'{
      cpus = { check_max( 32, 'cpus' ) }
      memory = { check_max( 256.GB * task.attempt, 'memory' ) }
-     time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
+    time = '365.d'
    }
   
   // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
 
   withName: makeSeqDict {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
       
   withName: fastqc {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: adapter_removal {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: samtools_flagstat {
@@ -82,10 +85,13 @@ process {
 
   withName: dedup {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: markduplicates {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    memory = { check_max( 20.GB * task.attempt, 'memory' ) }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
    
   withName: library_merge {
@@ -113,34 +119,43 @@ process {
 
   withName: maltextract {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: multivcfanalyzer {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: mtnucratio {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: vcf2genome {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: qualimap {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
    }
 
   withName: damageprofiler {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: circularmapper {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: circulargenerator {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
   withName: preseq {
@@ -150,6 +165,7 @@ process {
    
   withName: genotyping_ug {
     clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 2)}G,virtual_free=${(task.memory.toGiga() * 2)}G" }
+    errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } 
    }
 
 }
@@ -180,57 +196,53 @@ profiles {
         withLabel:'sc_tiny'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 1.5.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_small'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_medium'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 12.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_small'{
           cpus = { check_max( 2, 'cpus' ) }
           memory = { check_max( 6.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_medium' {
           cpus = { check_max( 4, 'cpus' ) }
           memory = { check_max( 12.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_large'{
           cpus = { check_max( 8, 'cpus' ) }
           memory = { check_max( 24.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_huge'{
           cpus = { check_max( 32, 'cpus' ) }
           memory = { check_max( 256.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         // Fixes for SGE and Java incompatibility due to  (and also some samtools?!) using more memory than you tell it to use
 
         withName: makeSeqDict {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
             
         withName: fastqc {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: adapter_removal {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: samtools_flagstat {
@@ -243,10 +255,13 @@ profiles {
 
         withName: dedup {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: markduplicates {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          memory = { check_max( 32.GB * task.attempt, 'memory' ) }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
         
         withName: library_merge {
@@ -270,47 +285,57 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
           cpus = { check_max( 32, 'cpus' ) }
           memory = { check_max( 955.GB * task.attempt, 'memory' ) }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
          }
 
         withName:hostremoval_input_fastq {
           memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-          time = 1440.h
         }
 
         withName: maltextract {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: multivcfanalyzer {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: mtnucratio {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: vcf2genome {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: qualimap {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
         }
 
         withName: damageprofiler {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: circularmapper {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: circulargenerator {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
         
         withName: genotyping_ug {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 3)}G,virtual_free=${(task.memory.toGiga() * 3)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: preseq {
@@ -345,57 +370,53 @@ profiles {
         withLabel:'sc_tiny'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 2.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_small'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'sc_medium'{
           cpus = { check_max( 1, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_small'{
           cpus = { check_max( 2, 'cpus' ) }
           memory = { check_max( 8.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_medium' {
           cpus = { check_max( 4, 'cpus' ) }
           memory = { check_max( 16.GB * task.attempt, 'memory' ) }
-          time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_large'{
            cpus = { check_max( 8, 'cpus' ) }
            memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
         }
 
         withLabel:'mc_huge'{
            cpus = { check_max( 32, 'cpus' ) }
            memory = { check_max( 512.GB * task.attempt, 'memory' ) }
-           time = { task.attempt == 3 ? 1440.h : task.attempt == 2 ? 48.h : 2.h }
          }
 
         // Fixes for SGE and Java incompatibility due to Java using more memory than you tell it to use
 
         withName: makeSeqDict {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
             
         withName: fastqc {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: adapter_removal {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: samtools_flagstat {
@@ -408,10 +429,13 @@ profiles {
 
         withName: dedup {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: markduplicates {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          memory = { check_max( 48.GB * task.attempt, 'memory' ) }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
         
         withName: library_merge {
@@ -430,7 +454,6 @@ profiles {
 
         withName:hostremoval_input_fastq {
           memory = { check_max( 32.GB * task.attempt, 'memory' ) }
-          time = 1440.h
         }
 
         withName: metagenomic_complexity_filter {
@@ -441,42 +464,53 @@ profiles {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=1000G,virtual_free=1000G" }
           cpus = { check_max( 32, 'cpus' ) }
           memory = { check_max( 955.GB * task.attempt, 'memory' ) }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
          }
 
         withName: maltextract {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: multivcfanalyzer {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: mtnucratio {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: vcf2genome {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: qualimap {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : task.exitStatus in [255] ? 'ignore' : 'finish' }
         }
 
         withName: damageprofiler {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          memory = { check_max( 32.GB * task.attempt, 'memory' ) }         
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: circularmapper {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
 
         withName: circulargenerator {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
         
         withName: genotyping_ug {
           clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toGiga() * 6)}G,virtual_free=${(task.memory.toGiga() * 6)}G" }
+          errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
         }
         
         withName: preseq {

conf/pipeline/viralrecon/genomes.config

@@ -51,6 +51,12 @@ params {
             primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4/SARS-CoV-2.scheme.bed'
             scheme     = 'SARS-CoV-2'
           }
+          '4.1' {
+            fasta      = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.reference.fasta'
+            gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'
+            primer_bed = 'https://github.com/artic-network/artic-ncov2019/raw/master/primer_schemes/nCoV-2019/V4.1/SARS-CoV-2.scheme.bed'
+            scheme     = 'SARS-CoV-2'
+          }          
           '1200' {
             fasta      = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/primer_schemes/artic/nCoV-2019/V1200/nCoV-2019.reference.fasta'
             gff        = 'https://github.com/nf-core/test-datasets/raw/viralrecon/genome/MN908947.3/GCA_009858895.3_ASM985889v3_genomic.200409.gff.gz'

docs/cbe.md

@@ -9,7 +9,7 @@ Before running the pipeline you will need to load Nextflow using the environment
 ```bash
 ## Load Nextflow environment module
 module purge
-module load nextflow/19.04.0
+module load nextflow/21.10.6
 ```
 
 A local copy of the [AWS-iGenomes](https://registry.opendata.aws/aws-igenomes/) resource has been made available on CBE so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. You can do this by simply using the `--genome <GENOME_ID>` parameter.

docs/czbiohub.md

@@ -125,7 +125,7 @@ For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annota
 
 ## High Priority Queue
 
-If you would like to run with the _High Priority_ queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
+If you would like to run with the *High Priority* queue, specify the `highpriority` config profile after `czbiohub_aws`. When applied after the main `czbiohub_aws` config, it overwrites the process `queue` identifier.
 
 To use it, submit your run with with `-profile czbiohub_aws,highpriority`.