Draft PR for the course

genomic-medicine-sweden · Oct 11, 2023 · c7d84f0 · c7d84f0
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diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 
 A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
 
-### Table of contents - 
+### Table of contents -
 - [Version updates](#Version-updates)
 - [Pipeline Diagram](#Pipeline-Diagram)
 - [Requirements](#Requirements)
@@ -22,20 +22,20 @@ A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinf
     - [Pipeline run command](#Manual-running-of-analysis-pipeline)
       - [Illumina pipeline](#Run-Illumina-pipeline)
       - [Nanopore pipeline](#Run-Nanopore-Pipeline)
-- [Useful information](#Useful-information) 
+- [Useful information](#Useful-information)
 ------------
 # Version updates
 ## v2.0.0
 ### Major updates
-- Docker container separated for Pangolin typing 
+- Docker container separated for Pangolin typing
     - Illumina container: [gms-artic-illumina](https://hub.docker.com/repository/docker/genomicmedicinesweden/gms-artic-illumina)
     - Nanopore container: [gms-artic-nanopore](https://hub.docker.com/repository/docker/genomicmedicinesweden/gms-artic-nanopore)
     - Pangolin container: [gms-artic-pangolin](https://hub.docker.com/repository/docker/genomicmedicinesweden/gms-artic-pangolin)
     - pycoQC container  : [pycoqc](https://hub.docker.com/repository/docker/jd21/pycoqc)
-- Added separate package version files for each workflow 
+- Added separate package version files for each workflow
     - versions: for Illumina and Nanopore
     - pangoversion: for pangolin typing
-- Illumina analysis additional features 
+- Illumina analysis additional features
     - flagstat
     - depth
     - VEP annotation
@@ -68,7 +68,7 @@ A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinf
 Find DAG and other figures [here](workflow-image/)
 
 # Requirements
-- Nextflow version >=20.10, <22.0 (tested OK on NextFlow version 20.10.0, version 21.10.6)
+- Nextflow version >=20.10
 - Singularity version 3.7.1 (tested OK)
 - Conda version >= 4.13.0 (tested OK)
 
@@ -146,7 +146,7 @@ nextflow run main.nf -profile singularity,sge \
 ```
 2. *for Illumina analysis*
 ```
-    sample_name     
+    sample_name
          |___ fastq/
 ```
 #### Run Illumina pipeline

diff --git a/conf/base.config b/conf/base.config
@@ -15,16 +15,18 @@ params{
     scheme = false
     tmpdir = "~/tmp"
 
-    
+
     // Repo to download your primer scheme from
+
     //schemeRepoURL = 'https://github.com/genomic-medicine-sweden/gms-artic.git'
-    schemeRepoURL = 'https://github.com/jd2112/gms-artic.git'
+    //schemeRepoURL = 'https://github.com/jd2112/gms-artic.git'
+    schemeRepoURL = 'https://github.com/artic-network/primer-schemes.git'
 
     // Directory within schemeRepoURL that contains primer schemes
-    schemeDir = 'gms-artic'
+    schemeDir = 'primer-schemes'
 
     // Scheme name
-    scheme = 'nCoV-2019-primer'
+    scheme = 'nCoV-2019'
 
     // Scheme version
     schemeVersion = 'V3'
@@ -37,7 +39,7 @@ params{
 
     // Run Illumina pipeline
     illumina = false
- 
+
     // Run nanopolish pipeline
     nanopolish = false
 

diff --git a/nextflow.config b/nextflow.config
@@ -42,163 +42,66 @@ profiles {
     docker.enabled = true
     fixOwnership = true
     runOptions = "-u \$(id -u):\$(id -g)"
+    params.tmpdir = "/tmp"
     if ( params.medaka || params.nanopolish ){
       process {
-        container="genomicmedicinesweden/gms-artic-nanopore:latest"
+        container="genomicmedicinesweden/gms-artic-nanopore:2023-06-21-p-4.3-d-1.20-c-0.1.11-s-0.3.17"
+        withName:pangolinTyping {
+          container="genomicmedicinesweden/gms-artic-pangolin:latest"
+        }
+        withName:pycoqc {
+          container="jd21/pycoqc:latest"
+       }
+       withName:pangoversions {
+            container = "genomicmedicinesweden/gms-artic-pangolin:latest"
+       }
+       withName:nextclade  {
+            container = "nextstrain/nextclade:latest"
+       }
+
       }
+
     }
     else {
-      process {
-        container="genomicmedicinesweden/gms-artic-illumina:latest"
-      }
-    }
+	 process {
+          container = "genomicmedicinesweden/gms-artic-illumina:latest"
+          withName:pangoversions {
+            container = "genomicmedicinesweden/gms-artic-pangolin:latest"
+          }
+          withName:pangolinTyping {
+            container = "genomicmedicinesweden/gms-artic-pangolin:latest"
+          }
+        }
+	}
   }
   singularity {
     singularity.enabled = true
     singularity.autoMounts = true
 
     if ( params.medaka || params.nanopolish ){
           process {
-        withName:articDownloadScheme {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:articGuppyPlex {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:articMinIONMedaka {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:articMinIONNanopolish {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:articRemoveUnmappedReads {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:makeQCCSV {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:writeQCSummaryCSV {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:collateSamples {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
+        container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
         withName:pangolinTyping {
           container="docker://genomicmedicinesweden/gms-artic-pangolin:latest"
         }
-        withName:nextclade {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:getVariantDefinitions {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:typeVariants {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:bamToCram {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:makeReport {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-        }
-        withName:fastqcNanopore {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-       }
-        withName:multiqcNanopore {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
-       }
         withName:pycoqc {
           container="docker://jd21/pycoqc:latest"
-       }
-        withName:versions {
-          container="docker://genomicmedicinesweden/gms-artic-nanopore:latest"
        }
        withName:pangoversions {
             container = "docker://genomicmedicinesweden/gms-artic-pangolin:latest"
        }
       }
     } else if (params.illumina) {
             process {
-          withName:articDownloadScheme {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:indexReference {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:versions {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:typeVariants {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
+          container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
           }
           withName:pangoversions {
             container = "docker://genomicmedicinesweden/gms-artic-pangolin:latest"
           }
-          withName:fastqc {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:readTrimming {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:readMapping {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:flagStat {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:trimPrimerSequences {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:depth {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:callConsensusFreebayes {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:annotationVEP {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:callVariants {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:makeConsensus {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:makeQCCSV {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:writeQCSummaryCSV {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:statsCoverage {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:statsInsert {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:statsAlignment {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:multiqc {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:collateSamples {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
           withName:pangolinTyping {
             container = "docker://genomicmedicinesweden/gms-artic-pangolin:latest"
           }
-          withName:nextclade {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:getVariantDefinitions {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
-          withName:makeReport {
-            container = "docker://genomicmedicinesweden/gms-artic-illumina:latest"
-          }
         }
-    }
     if (params.cache){
       singularity.cacheDir = params.cache
     }
@@ -227,19 +130,15 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline {
   enabled = true
-  file = "${params.tracedir}/execution_timeline.html"
 }
 report {
   enabled = true
-  file = "${params.tracedir}/execution_report.html"
 }
 trace {
   enabled = true
-  file = "${params.tracedir}/execution_trace.txt"
 }
 dag {
   enabled = false //requires graphic devices to run on ngp
-  file = "${params.tracedir}/pipeline_dag.svg"
 }
 
 manifest {