debug

guigolab · Oct 11, 2024 · 643c3b5 · 643c3b5
1 parent c6a5643
commit 643c3b5
Showing 1 changed file with 11 additions and 8 deletions.
diff --git a/.github/workflows/ncbi_all.yml b/.github/workflows/ncbi_all.yml
@@ -58,18 +58,21 @@ jobs:
       - name: Get new NCBI Assemblies
         run: |
           
-          query_result=query_result.tsv
-          ./datasets summary genome taxon "${{env.TAXID}}" --assembly-level chromosome,complete --annotated --as-json-lines |
-          ./dataformat tsv genome --fields "${{env.FIELDS}}" | 
-          tail -n +2 | head -n 10 > "$query_result"
+          # query_result=query_result.tsv
 
-          head -n 10 "$query_result"
+          ./datasets summary genome taxon "${{env.TAXID}}" --assembly-level chromosome,complete --annotated --as-json-lines |
+          ./dataformat tsv genome --fields "${{env.FIELDS}}" 
           
-          grep -vFf "${{env.EXISTING_ACCESSIONS}}" > "${{env.NEW_ACCESSIONS}}"
+          # | 
+          # tail -n +2 | head -n 10 > "$query_result"
+
+          # head -n 10 "$query_result"
+
+          # grep -vFf "${{env.EXISTING_ACCESSIONS}}" > "${{env.NEW_ACCESSIONS}}"
 
-          cat ${{env.NEW_ACCESSIONS}}"
+          # cat ${{env.NEW_ACCESSIONS}}"
 
-          rm ${{env.EXISTING_ACCESSIONS}}"
+          # rm ${{env.EXISTING_ACCESSIONS}}"
 
       - name: Set FTP paths
         run: |