update README

README.md

@@ -225,9 +225,10 @@ followed by `make map`.
 >    The labels are saved here: `intermediate/04_filter/labels`, and there you will find
 >    * CSV: in each row the first element is the query-id,
           the other values correspond to the labels of the filtered 
-          `intermediate/04_filter/all_queries.fa`, in the same order.
+          `intermediate/04_filter/{name}.fa`, in the same order.
 >    * json: keys are the filenames of files in `input/` (without extension), 
           for each filename, a list with the id of its sequences.
+>    * txt: consensus labels for each input file (majority vote among all labels from its sequences)
 ### 4e) Step 5: Analyze your results
 
 Check the output files in `output/` (for more info about formats, see
@@ -266,7 +267,7 @@ Here's a list of all implemented commands (to be executed as `make {command}`):
    download_asms      Download only the assemblies
    download_cobs      Download only the COBS indexes
    match              Match queries using COBS (queries -> candidates)
-   label              Label queries using labels from candidates (candidates -> labels)            *** [new command] ***
+   label              Label queries using labels from candidates (candidates -> labels) ** [new] **
    map                Map candidates to assemblies (candidates -> alignments)
 #############
 # Reporting #
@@ -315,8 +316,8 @@ are searched in the `input/` directory, as files with the following suffixes:
 
 **Output files:**
 
-* `output/all_queries.sam_summary.gz`: output alignments in a headerless SAM format
-* `output/all_queries.sam_summary.stats`: statistics about your computed alignments
+* `output/{name}.sam_summary.gz`: output alignments in a headerless SAM format
+* `output/{name}.sam_summary.stats`: statistics about your computed alignments
   in TSV
 
 
@@ -357,7 +358,3 @@ quite light and usually start running as soon as they are scheduled.
 
 * [Karel Brinda](https://brinda.eu) \<[email protected]\>
 * [Leandro Lima](https://github.com/leoisl) \<[email protected]\>
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-Test workflows