Merge pull request #5 from ebi-gene-expression-group/feature/update-p…

…yega Upgrade pyega
ebi-gene-expression-group · Jan 23, 2023 · ca06c53 · ca06c53
2 parents 0d1e38b + e986411
commit ca06c53
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/README.md b/README.md
@@ -4,8 +4,8 @@ This is a Nextflow workflow designed to download data for an EGA dataset and arr
 
 There are two operating modes:
 
- * Use the pyega3 client to pull files directly from EGA. This will only work for datasets without the older .gpg encryption, with all files using .cip.
- * Download files from a 'dropbox' provided to you from EGA staff. This is usually done where there are issues using the official client.
+ * Use the [pyega3](https://github.com/EGA-archive/ega-download-client) client to pull files directly from EGA. This will only work for datasets without the older .gpg encryption, with all files using .cip.
+ * Download files from a 'dropbox' provided to you from EGA staff. This is usually done where there are issues using the official client (this mode is currently deprecated).
 
 Note that there is no provision to use the old EGA Java client, which we have found difficult to use successfully.
 

diff --git a/main.nf b/main.nf
@@ -42,7 +42,7 @@ else{
 
         cache 'lenient'
 
-        conda 'pyega3'
+        conda 'pyega3>=5.0.1'
 
         input:
             set val(dsId), file(dsPath) from KEYED_DATASETS
@@ -162,6 +162,8 @@ else{
         errorStrategy { task.attempt<=3 ? 'retry' : 'ignore' }
 
         cache 'lenient'
+
+        conda 'pyega3>=5.0.1'
 
         maxForks 10