Update 20240306

.github/workflows/add_fastani_ref.yml

@@ -64,17 +64,23 @@ jobs:
             nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --fastani_ref_list fastani_ref_list.txt
 
             cat grandeur/grandeur_summary.tsv
+            cat grandeur/summary/software_versions.yml
+            ls  grandeur/multiqc/multiqc_report.html
 
         - name: Run Grandeur with refs
           run: |
             nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas -resume --fastani_ref GCA_009665515.2_ASM966551v2_genomic.fna.gz,GCA_009763645.1_ASM976364v1_genomic.fna.gz --outdir grandeur2
 
             cat grandeur2/grandeur_summary.tsv
+            cat grandeur2/summary/software_versions.yml
+            ls  grandeur2/multiqc/multiqc_report.html
 
         - name: Run Grandeur with refs and ref list
           run: |
             nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas -resume --fastani_ref_list fastani_ref_list.txt --fastani_ref GCA_009665515.2_ASM966551v2_genomic.fna.gz,GCA_009763645.1_ASM976364v1_genomic.fna.gz --outdir grandeur3
 
             cat grandeur3/grandeur_summary.tsv
+            cat grandeur3/summary/software_versions.yml
+            ls  grandeur3/multiqc/multiqc_report.html
 
 

.github/workflows/current.yml

@@ -33,3 +33,5 @@ jobs:
           nextflow run . -profile docker --current_datasets -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html

.github/workflows/ecoli.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check E. coli file
         run: |

.github/workflows/github_actions.config

@@ -1,31 +1,181 @@
 process {
-    maxRetries    = 0
-    maxErrors     = '-1'
-
-    withLabel:process_single {
-      cpus   = { 1 }
-      memory = { 6.GB * task.attempt }
-      time   = { 10.m * task.attempt }
-    }
-    withLabel:process_low {
-        cpus   = { 2     * task.attempt }
-        memory = { 12.GB * task.attempt }
-        time   = { 2.h   * task.attempt }
-    }
-    withLabel:process_medium {
-        cpus   = { 2     * task.attempt }
-        memory = { 12.GB * task.attempt }
+	maxRetries    = 0
+	maxErrors     = '-1'
+	
+	withLabel:process_single {
+		cpus   = { 1 }
+		memory = { 6.GB * task.attempt }
+		time   = { 10.m * task.attempt }
+	}
+	withLabel:process_low {
+		cpus   = { 2     * task.attempt }
+	    memory = { 12.GB * task.attempt }
+	    time   = { 2.h   * task.attempt }
+	}
+	withLabel:process_medium {
+		cpus   = { 2     * task.attempt }
+	    memory = { 12.GB * task.attempt }
         time   = { 4.h   * task.attempt }
     }
     withLabel:process_high {
-        cpus   = { 2    * task.attempt }
+        cpus   = { 2     * task.attempt }
         memory = { 12.GB * task.attempt }
         time   = { 16.h  * task.attempt }
     }
     withLabel:process_long {
         time   = { 20.h  * task.attempt }
-    }
-    withLabel:process_high_memory {
-        memory = { 12.GB * task.attempt }
-    }
-}
+	}
+	withLabel:process_high_memory {
+		memory = { 12.GB * task.attempt }
+	}
+
+	withName:amrfinderplus {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:bbduk {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:blastn {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:blobtools_create {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:blobtools_plot {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:blobtools_view {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:circulocov {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:core_genome_evaluation {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:datasets_download {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:datasets_summary {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:download_sra {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:drprg {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:elgato {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:emmtyper {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:fastani {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:fastp {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:fastqc {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:flag {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:heatcluster {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:iqtree2 {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:json_convert {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:kaptive {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:kleborate {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:kraken2 {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mash_dist {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mash_err {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mash_sketch_fasta {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mash_sketch_fastq {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mashtree {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mlst {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mqc_prep {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:multiqc {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:mykrobe {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:names {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:panaroo {
+		publishDir = [ path: "grandeur", mode: 'link', pattern: "panaroo/*"]
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:pbptyper {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:phytreeviz {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:plasmidfinder {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:prokka {
+		publishDir = [ path: "grandeur", mode: 'link', pattern: "gff/*.gff" ]
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:quast {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:references {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:seqsero2 {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:serotypefinder {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:shigatyper {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:snp_dists {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:spades {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:species {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:summary {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:versions {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+}

.github/workflows/klebsiella.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Klebsiella file
         run: |

.github/workflows/legionella.yml

@@ -36,6 +36,8 @@ jobs:
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Legionella file
         run: |

.github/workflows/myco.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Mycobacterium file
         run: |

.github/workflows/phylogenetic_workflow.yml

@@ -21,7 +21,7 @@ jobs:
         run: |
           docker --version
 
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          #wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
@@ -33,6 +33,8 @@ jobs:
           nextflow run . -profile docker,msa -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check MSA files
         run: |

.github/workflows/run_workflow.yml

@@ -29,6 +29,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --reads reads
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check summary files
         run: |

.github/workflows/salmonella.yml

@@ -38,6 +38,8 @@ jobs:
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fasta_list fastas.txt
 
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Salmonella file
         run: |

.github/workflows/strepA.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Strep pneumo file
         run: |

.github/workflows/strep_pneumo.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Strep pneumo file
         run: |

.github/workflows/test.yml

@@ -20,7 +20,7 @@ jobs:
       - name: Run Grandeur
         run: |
           nextflow run . -profile docker,test0 -c .github/workflows/github_actions.config
-
+          
       - name: Check contig files
         run: |
           for file in grandeur/contigs/*_contigs.fa

.github/workflows/vibrio.yml

@@ -35,6 +35,8 @@ jobs:
 
           nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check Vibrio species
         run: |

.github/workflows/withoutfastani.yml

@@ -21,7 +21,7 @@ jobs:
         run: |
           docker --version
 
-          wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
+          # wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/904/864/595/GCA_904864595.1_INF333/GCA_904864595.1_INF333_genomic.fna.gz             && gzip -d GCA_904864595.1_INF333_genomic.fna.gz
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/013/783/245/GCA_013783245.1_ASM1378324v1/GCA_013783245.1_ASM1378324v1_genomic.fna.gz && gzip -d GCA_013783245.1_ASM1378324v1_genomic.fna.gz
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/026/626/185/GCA_026626185.1_ASM2662618v1/GCA_026626185.1_ASM2662618v1_genomic.fna.gz && gzip -d GCA_026626185.1_ASM2662618v1_genomic.fna.gz 
           wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/020/808/985/GCA_020808985.1_ASM2080898v1/GCA_020808985.1_ASM2080898v1_genomic.fna.gz && gzip -d GCA_020808985.1_ASM2080898v1_genomic.fna.gz
@@ -33,11 +33,13 @@ jobs:
           nextflow run . -profile docker,msa -c .github/workflows/github_actions.config --fastas fastas --exclude_top_hit
 
           cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
 
       - name: Check MSA files
         run: |
           for file in grandeur/*/summary_statistics.txt grandeur/iqtree2/iqtree.treefile.nwk grandeur/snp-dists/snp_matrix.txt
           do
             head $file
             wc -l $file
-          done
+          done