added --no-check-certificate to all wgets

replikation · Dec 9, 2021 · 0c13952 · 0c13952
1 parent 9a5ad1c
commit 0c13952
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Showing 10 changed files with 13 additions and 13 deletions.
diff --git a/workflows/process/phage_annotation/download_pvog_DB.nf b/workflows/process/phage_annotation/download_pvog_DB.nf
@@ -9,13 +9,13 @@ process pvog_DB {
     script:
         if (task.attempt.toString() == '1')
         """
-        wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/hmmer_databases/pvogs.tar.gz && tar -zxvf pvogs.tar.gz
+        wget --no-check-certificate -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/hmmer_databases/pvogs.tar.gz && tar -zxvf pvogs.tar.gz
         rm pvogs.tar.gz
         """
 
         else if (task.attempt.toString() == '2')
         """
-        https://osf.io/n6ph5/download -O pvog.tar.gz
+        wget --no-check-certificate https://osf.io/n6ph5/download -O pvog.tar.gz
         tar -xvzf pvog.tar.gz
         cp -r pvog/pvogs/ .
         rm -r pvog

diff --git a/workflows/process/phage_annotation/download_vog_DB.nf b/workflows/process/phage_annotation/download_vog_DB.nf
@@ -6,7 +6,7 @@ process vog_DB {
         path("vogdb", type: 'dir')
     script:
         """
-        wget -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/hmmer_databases/vogdb.tar.gz && tar -zxvf vogdb.tar.gz
+        wget --no-check-certificate -nH ftp://ftp.ebi.ac.uk/pub/databases/metagenomics/viral-pipeline/hmmer_databases/vogdb.tar.gz && tar -zxvf vogdb.tar.gz
         rm vogdb.tar.gz
         """
 }
diff --git a/workflows/process/pprmeta/ppr_download_dependencies.nf b/workflows/process/pprmeta/ppr_download_dependencies.nf
@@ -14,7 +14,7 @@ process ppr_download_dependencies {
 
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/vchg9/download -O pprmeta.tar.gz
+        wget --no-check-certificate https://osf.io/vchg9/download -O pprmeta.tar.gz
         tar -xvzf pprmeta.tar.gz
         mv pprmeta/PPR-Meta/ .
         rm -r pprmeta/

diff --git a/workflows/process/sourmash/download_references.nf b/workflows/process/sourmash/download_references.nf
@@ -15,7 +15,7 @@ process download_references {
 
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/6ukfx/download -O references.tar.gz
+        wget --no-check-certificate https://osf.io/6ukfx/download -O references.tar.gz
         tar -xvzf references.tar.gz
         mv references/*.fa .
         rm -r references

diff --git a/workflows/process/sourmash/sourmash_download_DB.nf b/workflows/process/sourmash/sourmash_download_DB.nf
@@ -17,7 +17,7 @@ process sourmash_download_DB {
 
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/wm3gt/download -O sourmash.tar.gz
+        wget --no-check-certificate https://osf.io/wm3gt/download -O sourmash.tar.gz
         tar -xvzf sourmash.tar.gz
         mv sourmash/* .
         rm -r sourmash/

diff --git a/workflows/process/vibrant/vibrant_download_DB.nf b/workflows/process/vibrant/vibrant_download_DB.nf
@@ -21,7 +21,7 @@ process vibrant_download_DB {
 
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/j7435/download -O database.tar.gz
+        wget --no-check-certificate https://osf.io/j7435/download -O database.tar.gz
         """
 
 

diff --git a/workflows/process/vibrant_virome/vibrant_download_DB.nf b/workflows/process/vibrant_virome/vibrant_download_DB.nf
@@ -21,7 +21,7 @@ process vibrant_download_DB {
 
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/j7435/download -O database.tar.gz
+        wget --no-check-certificate https://osf.io/j7435/download -O database.tar.gz
         """
 
 

diff --git a/workflows/process/virsorter/virsorter_download_DB.nf b/workflows/process/virsorter/virsorter_download_DB.nf
@@ -9,13 +9,13 @@ process virsorter_download_DB {
     script:
         if (task.attempt.toString() == '1')
         """
-        wget https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz 
+        wget --no-check-certificate https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz 
         tar -xvzf virsorter-data-v2.tar.gz
         rm virsorter-data-v2.tar.gz
         """
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/qwzu3/download -O virsorter.tar.gz
+        wget --no-check-certificate https://osf.io/qwzu3/download -O virsorter.tar.gz
         tar -xvzf virsorter.tar.gz
         mv virsorter/virsorter-data/ .
         rm -r virsorter/

diff --git a/workflows/process/virsorter2/virsorter2_download_DB.nf b/workflows/process/virsorter2/virsorter2_download_DB.nf
@@ -6,7 +6,7 @@ process virsorter2_download_DB {
         path('db', type: 'dir')
     script:
         """
-        wget https://osf.io/v46sc/download -O db.tgz
+        wget --no-check-certificate https://osf.io/v46sc/download -O db.tgz
         tar -zxvf db.tgz
         chmod -R a+rX db
         rm db.tgz

diff --git a/workflows/process/virsorter_virome/virsorter_download_DB.nf b/workflows/process/virsorter_virome/virsorter_download_DB.nf
@@ -9,13 +9,13 @@ process virsorter_download_DB {
     script:
         if (task.attempt.toString() == '1')
         """
-        wget https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz 
+        wget --no-check-certificate https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz 
         tar -xvzf virsorter-data-v2.tar.gz
         rm virsorter-data-v2.tar.gz
         """
         else if (task.attempt.toString() == '2')
         """
-        wget https://osf.io/qwzu3/download -O virsorter.tar.gz
+        wget --no-check-certificate https://osf.io/qwzu3/download -O virsorter.tar.gz
         tar -xvzf virsorter.tar.gz
         mv virsorter/virsorter-data/ .
         rm -r virsorter/