From 0c13952c959afabe1a84a52bd9330aad0bcec78b Mon Sep 17 00:00:00 2001 From: mult1fractal Date: Thu, 9 Dec 2021 13:23:58 +0100 Subject: [PATCH] added --no-check-certificate to all wgets --- workflows/process/phage_annotation/download_pvog_DB.nf | 4 ++-- workflows/process/phage_annotation/download_vog_DB.nf | 2 +- workflows/process/pprmeta/ppr_download_dependencies.nf | 2 +- workflows/process/sourmash/download_references.nf | 2 +- workflows/process/sourmash/sourmash_download_DB.nf | 2 +- workflows/process/vibrant/vibrant_download_DB.nf | 2 +- workflows/process/vibrant_virome/vibrant_download_DB.nf | 2 +- workflows/process/virsorter/virsorter_download_DB.nf | 4 ++-- workflows/process/virsorter2/virsorter2_download_DB.nf | 2 +- workflows/process/virsorter_virome/virsorter_download_DB.nf | 4 ++-- 10 files changed, 13 insertions(+), 13 deletions(-) diff --git a/workflows/process/phage_annotation/download_pvog_DB.nf b/workflows/process/phage_annotation/download_pvog_DB.nf index 429f633..1db0db5 100644 --- 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 index 77dc216..39817fd 100644 --- 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 index 4e0bd34..be54a53 100644 --- 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 index c358ef8..b930384 100644 --- 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 index 84be3b6..8492379 100644 --- 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 index 6de0e96..36cf8bf 100644 --- 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 index 4256609..c3457d4 100644 --- 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 index d1eb62e..c7f05f9 100644 --- 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 index 60d6696..9d2f3b3 100644 --- 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 index d1eb62e..c7f05f9 100644 --- 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/