gzip patch

matsengrp · Jun 23, 2023 · a60f8eb · a60f8eb
1 parent 63e35f3
commit a60f8eb
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diff --git a/README.md b/README.md
@@ -16,10 +16,11 @@ various linux flavors
 
 Launch the pipeline execution with the following command: 
 
-    nextflow run matsengrp/phip-flow -r main -profile docker
+    nextflow run matsengrp/phip-flow -r V1.11 -profile docker
 
-Note: the ``-r main`` command runs the bleeding edge. For stable releases we recommend specifying
-on of the tags associated with a release (e.g. ``-r V1.10``). You may also specify any of the 
+Note: the ``-r VX.XX`` command runs the specified stable release version of the pipeline. 
+For running the bleeding edge (not generally recommended) you may also specify ``-r main``.
+You may also specify any of the 
 [parameters](https://matsengrp.github.io/phippery/alignments-pipeline.html#parameters) 
 for changing the input data and workflow behavior.
 

diff --git a/workflows/output.nf b/workflows/output.nf
@@ -11,7 +11,7 @@ process dump_tall_csv {
     shell:
     """
     phippery to-tall-csv -o ${params.dataset_prefix}-tall.csv $phip_data 
-    gzip *
+    gzip *.csv
     """
 }
 
@@ -23,7 +23,7 @@ process dump_wide_csv {
     shell:
     """
     phippery to-wide-csv -o $params.dataset_prefix $phip_data
-    gzip *
+    gzip *.csv
     """
 }
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,7 +11,7 @@ process dump_tall_csv { @@
         shell:
         """
         phippery to-tall-csv -o ${params.dataset_prefix}-tall.csv $phip_data
-        gzip *
+        gzip *.csv
         """
     }
@@ Expand All / @@ -23,7 +23,7 @@ process dump_wide_csv { @@
         shell:
         """
         phippery to-wide-csv -o $params.dataset_prefix $phip_data
-        gzip *
+        gzip *.csv
         """
     }
@@ Expand Down @@