added software versions and multiqc

UPHL-BioNGS · Mar 12, 2024 · 38dae3d · 38dae3d
1 parent 9d42197
commit 38dae3d
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Showing 14 changed files with 34 additions and 1 deletion.
diff --git a/.github/workflows/add_fastani_ref.yml b/.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
 
 
diff --git a/.github/workflows/current.yml b/.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
diff --git a/.github/workflows/ecoli.yml b/.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: |

diff --git a/.github/workflows/klebsiella.yml b/.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: |

diff --git a/.github/workflows/legionella.yml b/.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: |

diff --git a/.github/workflows/myco.yml b/.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: |

diff --git a/.github/workflows/phylogenetic_workflow.yml b/.github/workflows/phylogenetic_workflow.yml
@@ -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: |

diff --git a/.github/workflows/run_workflow.yml b/.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: |

diff --git a/.github/workflows/salmonella.yml b/.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: |

diff --git a/.github/workflows/strepA.yml b/.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: |

diff --git a/.github/workflows/strep_pneumo.yml b/.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: |

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -20,7 +20,10 @@ jobs:
       - name: Run Grandeur
         run: |
           nextflow run . -profile docker,test0 -c .github/workflows/github_actions.config
-      
+          cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
+          
       - name: Check contig files
         run: |
           for file in grandeur/contigs/*_contigs.fa

diff --git a/.github/workflows/vibrio.yml b/.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: |

diff --git a/.github/workflows/withoutfastani.yml b/.github/workflows/withoutfastani.yml
@@ -33,6 +33,8 @@ 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: |