Merge pull request #248 from UPHL-BioNGS/adding_meningotype

Adding meningotype
UPHL-BioNGS · Jan 29, 2025 · b718289 · b718289
2 parents ca81699 + 15961fb
commit b718289
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diff --git a/.github/workflows/add_fastani_ref.yml b/.github/workflows/add_fastani_ref.yml
@@ -61,26 +61,30 @@ jobs:
 
         - name: Run Grandeur with ref list
           run: |
-            nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --fastani_ref_list fastani_ref_list.txt
+            nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --fastani_ref_list fastani_ref_list.txt --publish_dir_mode link
 
             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
+            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 --publish_dir_mode link
   
             cat grandeur2/grandeur_summary.tsv
             cat grandeur2/summary/software_versions.yml
             ls  grandeur2/multiqc/multiqc_report.html
 
+        - name: Clean up Disk space
+          uses: jlumbroso/free-disk-space@main
+
         - 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
+            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 --publish_dir_mode link
     
             cat grandeur3/grandeur_summary.tsv
             cat grandeur3/summary/software_versions.yml
             ls  grandeur3/multiqc/multiqc_report.html
 
-
+        - name: tree
+          run: tree grandeur*
diff --git a/.github/workflows/current.yml b/.github/workflows/current.yml
@@ -10,17 +10,21 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@main
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
 
           nextflow -version
-          
-      - name: Run Grandeur
-        run: |
-          docker --version
 
+      - name: Test docker
+        run: docker --version
+
+      - name: Get files
+        run: |
           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 
@@ -30,8 +34,16 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker --current_datasets -c .github/workflows/github_actions.config --fastas fastas
+      - name: Run Grandeur
+        run: |
+          nextflow run . -profile docker --current_datasets -c .github/workflows/github_actions.config --fastas fastas --publish_dir_mode link
 
+      - name: Check files
+        run: |
           cat grandeur/grandeur_summary.tsv
           cat grandeur/summary/software_versions.yml
           ls  grandeur/multiqc/multiqc_report.html
+
+      - name: tree
+        run: tree grandeur*
+
diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -10,6 +10,9 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@main
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -33,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --publish_dir_mode link
           cat grandeur/grandeur_summary.tsv
           cat grandeur/summary/software_versions.yml
           ls  grandeur/multiqc/multiqc_report.html
@@ -45,4 +48,6 @@ jobs:
             head $file
             wc -l $file
           done
-  
+
+      - name: tree
+        run: tree grandeur*
diff --git a/.github/workflows/gc.yml b/.github/workflows/gc.yml
@@ -0,0 +1,54 @@
+name: Test Grandeur workflow with Neisseria meningitidis
+
+on: [pull_request, workflow_dispatch]
+
+jobs:
+
+  test:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@main
+
+      - name: Install Nextflow
+        run: |
+          wget -qO- get.nextflow.io | bash
+          sudo mv nextflow /usr/local/bin/
+
+          nextflow -version
+          
+      - name: Run Grandeur
+        run: |
+          docker --version
+          
+          mkdir fastas 
+          for accession in GCA_022869645.1_ASM2286964v1
+          do
+            all=$(echo $accession | cut -f 2 -d "_")
+            fir=$(echo $all | cut -c 1-3)
+            mid=$(echo $all | cut -c 4-6)
+            end=$(echo $all | cut -c 7-9)
+            wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/${fir}/${mid}/${end}/${accession}/${accession}_genomic.fna.gz
+            gzip -d ${accession}_genomic.fna.gz
+            mv ${accession}_genomic.fna fastas/.
+          done
+
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas --publish_dir_mode link
+          cat grandeur/grandeur_summary.tsv
+          cat grandeur/summary/software_versions.yml
+          ls  grandeur/multiqc/multiqc_report.html
+
+      - name: Check Neisseria file
+        run: |
+          for file in grandeur/meningotype/meningotype_summary.tsv
+          do
+            head $file
+            wc -l $file
+          done
+
+          
+      - name: tree
+        run: tree grandeur*
diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config
@@ -29,153 +29,153 @@ process {
 		memory = { 12.GB * task.attempt }
 	}
 
-	withName:amrfinderplus {
+	withName:AMRFINDER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:bbduk {
+	withName:BAKTA {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:blastn {
+	withName:BLASTN {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:blobtools_create {
+	withName:BLOBTOOLS_CREATE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:blobtools_plot {
+	withName:BLOBTOOLS_PLOT {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:blobtools_view {
+	withName:BLOBTOOLS_VIEW {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:circulocov {
+	withName:CIRCULOCOV {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:core_genome_evaluation {
+	withName:CORE_GENOME_EVALUATION {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:datasets_download {
+	withName:DATASETS_DOWNLOAD {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:datasets_summary {
+	withName:DATASETS_SUMMARY {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:download_sra {
+	withName:DOWNLOAD_SRA {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:drprg {
+	withName:DRPRG {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:elgato {
+	withName:ELGATO {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:emmtyper {
+	withName:EMMTYPER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:fastani {
+	withName:ENA_DOWNLOAD {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:fastp {
+	withName:FASTANI {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:fastqc {
+	withName:FASTP {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:flag {
+	withName:FASTQC {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:heatcluster {
+	withName:HEATCLUSTER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:iqtree2 {
+	withName:IQTREE2 {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:json_convert {
+	withName:JSON_CONVERT {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:kaptive {
+	withName:KAPTIVE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:kleborate {
+	withName:KLEBORATE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:kraken2 {
+	withName:KRAKEN2 {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mash_dist {
+	withName:MASHTREE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mash_err {
+	withName:MASH_DIST {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mash_sketch_fasta {
+	withName:MASH_SKETCH {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mash_sketch_fastq {
+	withName:MENINGOTYPE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mashtree {
+	withName:MLST {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mlst {
+	withName:MQC_PREP {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mqc_prep {
+	withName:MULTIQC {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:multiqc {
+	withName:MYKROBE {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:mykrobe {
+	withName:NAMES {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:names {
-		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
-	}
-	withName:panaroo {
+	withName:PANAROO {
 		publishDir = [ path: "grandeur", mode: 'link', pattern: "panaroo/*"]
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:pbptyper {
+	withName:PBPTYPER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:phytreeviz {
+	withName:PHYTREEVIZ {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:plasmidfinder {
+	withName:PLASMIDFINDER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:prokka {
+	withName:PROKKA {
 		publishDir = [ path: "grandeur", mode: 'link', pattern: "gff/*.gff" ]
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:quast {
+	withName:QUAST {
+		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
+	}
+	withName:REFERENCES {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:references {
+	withName:ROARY {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:seqsero2 {
+	withName:SEQSERO2 {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:serotypefinder {
+	withName:SEROTYPEFINDER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:shigatyper {
+	withName:SHIGATYPER {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:snp_dists {
+	withName:SNPDISTS {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:spades {
+	withName:SPADES {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:species {
+	withName:SPECIES {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:summary {
+	withName:SUMMARY {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
-	withName:versions {
+	withName:VERSIONS {
 		errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'}
 	}
 }
diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
@@ -10,6 +10,9 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@main
+
       - name: Install Nextflow
         run: |
           wget -qO- get.nextflow.io | bash
@@ -30,7 +33,7 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker,just_msa -c .github/workflows/github_actions.config --fastas fastas
+          nextflow run . -profile docker,just_msa -c .github/workflows/github_actions.config --fastas fastas --publish_dir_mode link
 
       - name: Check MSA files
         run: |
@@ -39,3 +42,6 @@ jobs:
             head $file
             wc -l $file
           done
+
+      - name: tree
+        run: tree grandeur*