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added --no-check-certificate to wgets
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@mult1fractal
mult1fractal committed May 11, 2022
1 parent 1e53b61 commit 928cd60
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Showing 15 changed files with 20 additions and 20 deletions.
2 changes: 1 addition & 1 deletion workflows/process/checkV/download_checkV_DB.nf
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Expand Up @@ -7,7 +7,7 @@ process download_checkV_DB {
path("checkv-db-v*", type: 'dir')
script:
"""
wget https://portal.nersc.gov/CheckV/checkv-db-v0.6.tar.gz
wget --no-check-certificate https://portal.nersc.gov/CheckV/checkv-db-v0.6.tar.gz
tar -zxvf checkv-db-v0.6.tar.gz
rm checkv-db-v0.6.tar.gz
"""
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2 changes: 1 addition & 1 deletion workflows/process/metaphinder_own_DB/download_references.nf
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Expand Up @@ -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
cp references/*.fa .
rm -r references
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2 changes: 1 addition & 1 deletion workflows/process/metaphinder_own_DB/phage_references_blastDB.nf
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Expand Up @@ -18,7 +18,7 @@ process phage_references_blastDB {

else if (task.attempt.toString() == '2')
"""
wget https://osf.io/7gcky/download -O blast_database.tar.gz
wget --no-check-certificate https://osf.io/7gcky/download -O blast_database.tar.gz
"""

stub:
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8 changes: 4 additions & 4 deletions workflows/process/phage_annotation/download_pvog_DB.nf
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Expand Up @@ -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
Expand Down Expand Up @@ -44,9 +44,9 @@ process vogtable_DB {

// else if (task.attempt.toString() == '2')
"""
## wget https://osf.io/nr6yb/download -O VOGTable.txt
## wget --no-check-certificate https://osf.io/nr6yb/download -O VOGTable.txt
wget https://osf.io/9n75g/download -O vog_table.tar.gz
wget --no-check-certificate https://osf.io/9n75g/download -O vog_table.tar.gz
tar -xvzf vog_table.tar.gz
mv vog_table/*.txt .
rm vog_table.tar.gz
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2 changes: 1 addition & 1 deletion workflows/process/phage_annotation/download_vog_DB.nf
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Expand Up @@ -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
"""
}
2 changes: 1 addition & 1 deletion workflows/process/phage_tax_classification/download_references.nf
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Expand Up @@ -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
cp references/*.fa .
rm -r references/
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2 changes: 1 addition & 1 deletion workflows/process/phage_tax_classification/sourmash_download_DB.nf
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Expand Up @@ -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/
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2 changes: 1 addition & 1 deletion workflows/process/pprmeta/ppr_download_dependencies.nf
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Expand Up @@ -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/
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2 changes: 1 addition & 1 deletion workflows/process/sourmash/download_references.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion workflows/process/sourmash/sourmash_download_DB.nf
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Expand Up @@ -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/
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2 changes: 1 addition & 1 deletion workflows/process/vibrant/vibrant_download_DB.nf
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Expand Up @@ -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
"""


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2 changes: 1 addition & 1 deletion workflows/process/vibrant_virome/vibrant_download_DB.nf
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Expand Up @@ -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
"""


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4 changes: 2 additions & 2 deletions workflows/process/virsorter/virsorter_download_DB.nf
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Expand Up @@ -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/
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2 changes: 1 addition & 1 deletion workflows/process/virsorter2/virsorter2_download_DB.nf
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Expand Up @@ -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
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4 changes: 2 additions & 2 deletions workflows/process/virsorter_virome/virsorter_download_DB.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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/
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