amend

cmkobel · Jul 25, 2024 · 480fb26 · 480fb26
1 parent e7005b9
commit 480fb26
Show file tree

Hide file tree

Showing 2 changed files with 17 additions and 2 deletions.
diff --git a/changelog.txt b/changelog.txt
@@ -1,6 +1,7 @@
 2.10.1
   - Breaking change: New Docker image (pinned eggnog)
   - Variation in output files from Eggnog means that eggnog is now pinned to v2.1.12. Thanks to @michoug
+  - Quiet report output
   - Minor fixes.
 
 2.9.1

diff --git a/comparem2 b/comparem2
@@ -127,7 +127,7 @@ logger.debug(f"The concatenated trailing arguments are {trailing_arguments_conca
 command_main = f"snakemake --snakefile \"{COMPAREM2_BASE}\"/workflow/Snakefile --profile \"{COMPAREM2_PROFILE}\" --configfile \"{COMPAREM2_BASE}\"/config/config.yaml  " + trailing_arguments_concatenated
 logger.debug(f"Command to run is\n{command_main}")
 
-command_report = f"""snakemake --snakefile "$COMPAREM2_BASE/dynamic_report/workflow/Snakefile" --profile "$COMPAREM2_PROFILE" --configfile=.report_config.yaml"""
+command_report = f"""snakemake --snakefile "$COMPAREM2_BASE/dynamic_report/workflow/Snakefile" --profile "$COMPAREM2_PROFILE" --configfile=.report_config.yaml --quiet all"""
 
 
 
@@ -145,7 +145,21 @@ elif "--help" in trailing_arguments or "-h" in trailing_arguments:
 
 
 elif "--cite" in trailing_arguments:
-    print("If you use CompareM2, you can support further funding by bumping the citation count on this one:\n\n\tKobel, C. M. et al. CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. 2024.07.12.603264 Preprint at https://doi.org/10.1101/2024.07.12.603264 (2024).\n\nCompareM2 would not have existed, if it hadn't been for the integrated software packages and their databases. Please cite the appropriate tools as well. An updated list is maintained here: https://comparem2.readthedocs.io/en/latest/99%20citation/\n")
+    print("""
+  CompareM2 Citation
+  ------------------
+
+  If you use CompareM2, you can support further funding by bumping the
+  citation count on this one:
+
+    - Kobel, C. M. et al. CompareM2 is a genomes-to-report pipeline for comparing microbial genomes. 2024.07.12.603264 Preprint at https://doi.org/10.1101/2024.07.12.603264 (2024).
+
+  CompareM2 would not have existed, if it hadn't been for the
+  integrated software packages and their databases. Please cite the
+  appropriate tools as well. An updated list is maintained here:
+
+    - https://comparem2.readthedocs.io/en/latest/99%20citation/
+""")
 
 
 else: