From 5d9744f98968c41f59312820f3c0da5706ab5ff6 Mon Sep 17 00:00:00 2001 From: Kirill Bessonov Date: Tue, 1 Oct 2024 16:21:38 -0400 Subject: [PATCH] Updated README.md and CHANGELOG.md --- README.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/README.rst b/README.rst index 1a9e1d2..53736d1 100644 --- a/README.rst +++ b/README.rst @@ -306,12 +306,14 @@ Tab-delimited results output (``-f tab``): CSV results output (``-f csv``): ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Raw ``csv`` output results opened in a text editor + .. code-block:: csv cgmlst_ST,cgmlst_distance,cgmlst_genome_match,cgmlst_matching_alleles,cgmlst_subspecies,fasta_filepath,genome,h1,h2,o_antigen,qc_messages,qc_status,serogroup,serovar,serovar_antigen,serovar_cgmlst 660408169,0.00909090909091,LT2,327,enterica,/home/peter/Downloads/sistr-LT2-example/LT2.fasta,LT2,i,"1,2","1,4,[5],12",,PASS,B,Typhimurium,Typhimurium,Typhimurium The same ``csv`` results rendered as a table + .. csv-table:: cgmlst_ST,cgmlst_distance,cgmlst_genome_match,cgmlst_matching_alleles,cgmlst_subspecies,fasta_filepath,genome,h1,h2,o_antigen,qc_messages,qc_status,serogroup,serovar,serovar_antigen,serovar_cgmlst @@ -437,7 +439,7 @@ Example: Here's some truncated example allele search results output in JSON format for ``LT2`` sample: -.. code-block:: json +.. code-block:: text { "LT2": { @@ -523,7 +525,7 @@ The QC messages produced by ``sistr_cmd`` should help you understand your serova Galaxy workflows ================ -The `galaxy `_ folder contains Galaxy Project SISTR workflows that allow to process samples in large batches. +The `galaxy `_ folder contains Galaxy SISTR workflows that can be readily imported into existing Galaxy server instance and allow to process WGS samples in large batches starting from raw reads and finishing with serovar results. - `Galaxy-Workflow-Assembly-Serotyping-withReport-for-SISTR_v1.1.1+galaxy1-recipe.ga `_