added path to files

UPHL-BioNGS · Feb 13, 2024 · 250b4cb · 250b4cb
1 parent f45d9e6
commit 250b4cb
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Showing 13 changed files with 14 additions and 13 deletions.
diff --git a/.github/workflows/current.yml b/.github/workflows/current.yml
@@ -33,6 +33,6 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker --current_datasets -c .github/workflows/github_actions.config
+          nextflow run . -profile docker --current_datasets -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
diff --git a/.github/workflows/ecoli.yml b/.github/workflows/ecoli.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
           
       - name: Check E. coli file

diff --git a/.github/workflows/just_msa.yml b/.github/workflows/just_msa.yml
@@ -33,7 +33,7 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker,just_msa -c .github/workflows/github_actions.config
+          nextflow run . -profile docker,just_msa -c .github/workflows/github_actions.config --fastas fastas
 
       - name: Check MSA files
         run: |

diff --git a/.github/workflows/klebsiella.yml b/.github/workflows/klebsiella.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
 
       - name: Check Klebsiella file

diff --git a/.github/workflows/legionella.yml b/.github/workflows/legionella.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           
           cat grandeur/grandeur_summary.tsv
 

diff --git a/.github/workflows/myco.yml b/.github/workflows/myco.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
 
       - name: Check Mycobacterium file

diff --git a/.github/workflows/phylogenetic_workflow.yml b/.github/workflows/phylogenetic_workflow.yml
@@ -37,7 +37,7 @@ jobs:
 
           cat grandeur/grandeur_summary.tsv
 
-          nextflow run . -profile docker,msa -resume -c .github/workflows/github_actions.config
+          nextflow run . -profile docker,msa -resume -c .github/workflows/github_actions.config --fastas fastas
 
       - name: Check MSA files
         run: |

diff --git a/.github/workflows/run_workflow.yml b/.github/workflows/run_workflow.yml
@@ -29,7 +29,8 @@ jobs:
           wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_1.fastq.gz
           wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/002/SRR2838702/SRR2838702_2.fastq.gz
           mv *fastq.gz reads/.
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --reads reads
           cat grandeur/grandeur_summary.tsv
       
       - name: Check summary files

diff --git a/.github/workflows/salmonella.yml b/.github/workflows/salmonella.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv
 

diff --git a/.github/workflows/strepA.yml b/.github/workflows/strepA.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
 
       - name: Check Strep pneumo file

diff --git a/.github/workflows/strep_pneumo.yml b/.github/workflows/strep_pneumo.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
 
       - name: Check Strep pneumo file

diff --git a/.github/workflows/vibrio.yml b/.github/workflows/vibrio.yml
@@ -36,7 +36,7 @@ jobs:
             mv ${accession}_genomic.fna fastas/.
           done
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
           cat grandeur/grandeur_summary.tsv
 
       - name: Check Vibrio species

diff --git a/.github/workflows/withoutfastani.yml b/.github/workflows/withoutfastani.yml
@@ -33,7 +33,7 @@ jobs:
           mkdir fastas
           mv *fna fastas/.
 
-          nextflow run . -profile docker -c .github/workflows/github_actions.config
+          nextflow run . -profile docker -c .github/workflows/github_actions.config --fastas fastas
 
           cat grandeur/grandeur_summary.tsv