Fix provenance format (#18)

BCCDC-PHL · Feb 20, 2024 · 40ee459 · 40ee459
1 parent 6018ee5
commit 40ee459
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Showing 4 changed files with 19 additions and 8 deletions.
diff --git a/modules/hash_files.nf b/modules/hash_files.nf
@@ -13,7 +13,9 @@ process hash_files {
     """
     shasum -a 256 ${files_to_hash} | tr -s ' ' ',' > ${sample_id}_${file_type}.sha256.csv
     while IFS=',' read -r hash filename; do
-      printf -- "- input_filename: \$filename\\n  input_path: \$(realpath \$filename)\\n  sha256: \$hash\\n" >> ${sample_id}_${file_type}_provenance.yml
+        printf -- "- input_filename: \$filename\\n"          >> ${sample_id}_${file_type}_provenance.yml
+        printf -- "  input_path: \$(realpath \$filename)\\n" >> ${sample_id}_${file_type}_provenance.yml
+        printf -- "  sha256: \$hash\\n"                      >> ${sample_id}_${file_type}_provenance.yml
     done < ${sample_id}_${file_type}.sha256.csv
     """
 }
diff --git a/modules/mlst.nf b/modules/mlst.nf
@@ -13,11 +13,18 @@ process mlst {
 
     script:
     """
-    printf -- "- process_name: mlst\\n" > ${sample_id}_mlst_provenance.yml
-    printf -- "  tool_name: mlst\\n  tool_version: \$(mlst --version | cut -d ' ' -f 2)\\n  parameters:\\n" >> ${sample_id}_mlst_provenance.yml
-    printf -- "  - parameter: minid\\n    value: ${params.minid}\\n" >> ${sample_id}_mlst_provenance.yml
-    printf -- "  - parameter: mincov\\n    value: ${params.mincov}\\n" >> ${sample_id}_mlst_provenance.yml
-    printf -- "  - parameter: minscore\\n    value: ${params.minscore}\\n" >> ${sample_id}_mlst_provenance.yml
+    printf -- "- process_name: mlst\\n"                                     >> ${sample_id}_mlst_provenance.yml
+    printf -- "  tools:\\n"                                                 >> ${sample_id}_mlst_provenance.yml
+    printf -- "    - tool_name: mlst\\n"                                    >> ${sample_id}_mlst_provenance.yml
+    printf -- "      tool_version: \$(mlst --version | cut -d ' ' -f 2)\\n" >> ${sample_id}_mlst_provenance.yml
+    printf -- "      parameters:\\n"                                        >> ${sample_id}_mlst_provenance.yml
+    printf -- "      - parameter: minid\\n"                                 >> ${sample_id}_mlst_provenance.yml
+    printf -- "        value: ${params.minid}\\n"                           >> ${sample_id}_mlst_provenance.yml
+    printf -- "      - parameter: mincov\\n"                                >> ${sample_id}_mlst_provenance.yml
+    printf -- "        value: ${params.mincov}\\n"                          >> ${sample_id}_mlst_provenance.yml
+    printf -- "      - parameter: minscore\\n"                              >> ${sample_id}_mlst_provenance.yml
+    printf -- "        value: ${params.minscore}\\n"                        >> ${sample_id}_mlst_provenance.yml
+
     mlst \
       --minid ${params.minid} \
       --mincov ${params.mincov} \

diff --git a/modules/provenance.nf b/modules/provenance.nf
@@ -32,6 +32,8 @@ process pipeline_provenance {
 
   script:
   """
-  printf -- "- pipeline_name: ${pipeline_name}\\n  pipeline_version: ${pipeline_version}\\n- timestamp_analysis_start: ${analysis_start}\\n" > pipeline_provenance.yml
+  printf -- "- pipeline_name: ${pipeline_name}\\n"             >> pipeline_provenance.yml
+  printf -- "  pipeline_version: ${pipeline_version}\\n"       >> pipeline_provenance.yml
+  printf -- "  timestamp_analysis_start: ${analysis_start}\\n" >> pipeline_provenance.yml
   """
 }
diff --git a/nextflow.config b/nextflow.config
@@ -1,7 +1,7 @@
 manifest {
   author = 'Dan Fornika'
   name = 'BCCDC-PHL/mlst-nf'
-  version = '0.1.3'
+  version = '0.1.4'
   description = 'BCCDC-PHL MLST'
   mainScript = 'main.nf'
   nextflowVersion = '>=20.01.0'