diff --git a/bin/gtdb_download.sh b/bin/gtdb_download.sh index 8ee64208..87c95533 100755 --- a/bin/gtdb_download.sh +++ b/bin/gtdb_download.sh @@ -25,7 +25,7 @@ then mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=${DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- ${DOWNLOAD_LINK} | tar xvz " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- ${DOWNLOAD_LINK} | tar xvz " \ --s3FileCommand="s5cmd ${S5CMD_PARAMS} cat ${DOWNLOAD_LINK} | tar xzv " \ --s3DirectoryCommand="s5cmd ${S5CMD_PARAMS} cp ${DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="${S5CMD_PARAMS}" \ diff --git a/bin/wgetStatic b/bin/wgetStatic new file mode 100755 index 00000000..a1a923ca Binary files /dev/null and b/bin/wgetStatic differ diff --git a/modules/annotation/module.nf b/modules/annotation/module.nf index d3651fea..690728d9 100644 --- a/modules/annotation/module.nf +++ b/modules/annotation/module.nf @@ -163,7 +163,7 @@ process pMMseqs2_taxonomy { # If a database is present at the given path, checksums are compared, if they are identical the download will be omitted. flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE}/!{dbType} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -c -d | tar -xv " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -c -d | tar -xv " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -c -d | tar -xv " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ @@ -270,7 +270,7 @@ process pResistanceGeneIdentifier { mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | tar -xvj " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | tar -xvj " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} !{DOWNLOAD_LINK} | tar -xvj " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ @@ -482,7 +482,7 @@ process pKEGGFromMMseqs2 { mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | tar -xz " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | tar -xz " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat !{DOWNLOAD_LINK} | tar -xz " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/modules/plasmids/processes.nf b/modules/plasmids/processes.nf index e7f6c8ed..35ad570f 100644 --- a/modules/plasmids/processes.nf +++ b/modules/plasmids/processes.nf @@ -70,7 +70,7 @@ process pViralVerifyPlasmid { mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | pigz -fdc > pfam.hmm " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | pigz -fdc > pfam.hmm " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} !{DOWNLOAD_LINK} | pigz -fdc > pfam.hmm " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . && mv * pfam.hmm " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ @@ -235,7 +235,7 @@ process pPlaton { mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | tar -xvz " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | tar -xvz " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat !{DOWNLOAD_LINK} | tar -xvz " \ --s3DirectoryCommand="mkdir db && cd db && s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/templates/checkm.sh b/templates/checkm.sh index 385f4fb7..61972b38 100644 --- a/templates/checkm.sh +++ b/templates/checkm.sh @@ -22,7 +22,7 @@ then mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | tar -xzv " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | tar -xzv " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} !{DOWNLOAD_LINK} | tar -xzv " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/templates/checkm2.sh b/templates/checkm2.sh index 689686a4..53d6a9d4 100644 --- a/templates/checkm2.sh +++ b/templates/checkm2.sh @@ -20,7 +20,7 @@ then mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -O checkm2.tar.gz !{DOWNLOAD_LINK} && tar -xzvf checkm2.tar.gz && rm checkm2.tar.gz" \ + --httpsCommand="wgetStatic --no-check-certificate -O checkm2.tar.gz !{DOWNLOAD_LINK} && tar -xzvf checkm2.tar.gz && rm checkm2.tar.gz" \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} checkm2.tar.gz && tar -xzvf checkm2.tar.gz && rm checkm2.tar.gz" \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/templates/mmseqs2.sh b/templates/mmseqs2.sh index 26f73cbc..9587391f 100644 --- a/templates/mmseqs2.sh +++ b/templates/mmseqs2.sh @@ -19,7 +19,7 @@ then # If a database is present at the given path, checksums are compared. If they are identical, the download will be omitted. flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE}/!{dbType} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand="wget -qO- !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -d -c | tar -xv " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -d -c | tar -xv " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} !{DOWNLOAD_LINK} | zstd -T!{task.cpus} -d -c | tar -xv " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/templates/mobtyper.sh b/templates/mobtyper.sh index fd31c6ab..582cd471 100644 --- a/templates/mobtyper.sh +++ b/templates/mobtyper.sh @@ -19,7 +19,7 @@ then mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=!{DOWNLOAD_LINK} \ - --httpsCommand=" wget -qO- !{DOWNLOAD_LINK} | tar --strip-components=1 -xvz " \ + --httpsCommand=" wgetStatic --no-check-certificate -qO- !{DOWNLOAD_LINK} | tar --strip-components=1 -xvz " \ --s3FileCommand=" s5cmd !{S5CMD_PARAMS} cat !{DOWNLOAD_LINK} | tar --strip-components=1 -xvz " \ --s3DirectoryCommand=" s5cmd !{S5CMD_PARAMS} cp !{DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \ diff --git a/templates/plsdb.sh b/templates/plsdb.sh index 0579f6eb..b8809498 100644 --- a/templates/plsdb.sh +++ b/templates/plsdb.sh @@ -21,7 +21,7 @@ then mkdir -p ${DATABASE} flock ${LOCK_FILE} concurrentDownload.sh --output=${DATABASE} \ --link=$DOWNLOAD_LINK \ - --httpsCommand="wget -qO- $DOWNLOAD_LINK | tar xjv " \ + --httpsCommand="wgetStatic --no-check-certificate -qO- $DOWNLOAD_LINK | tar xjv " \ --s3FileCommand="s5cmd !{S5CMD_PARAMS} cat --concurrency !{task.cpus} ${DOWNLOAD_LINK} | tar xjv " \ --s3DirectoryCommand="s5cmd !{S5CMD_PARAMS} cp --concurrency !{task.cpus} ${DOWNLOAD_LINK} . " \ --s5cmdAdditionalParams="!{S5CMD_PARAMS}" \