Merge branch 'dev' into feature/add-tpm-rpkm-matrix

metagenomics · May 24, 2024 · 1b5830e · 1b5830e
2 parents fad6238 + 7b7e31c
commit 1b5830e
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Showing 9 changed files with 11 additions and 11 deletions.
diff --git 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
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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}" \