Remove compressed flags from all mmmseqs modules

nf-core · Dec 12, 2024 · b886a8b · b886a8b
1 parent b5828f4
commit b886a8b
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Showing 9 changed files with 8 additions and 18 deletions.
diff --git a/modules/nf-core/mmseqs/cluster/main.nf b/modules/nf-core/mmseqs/cluster/main.nf
@@ -34,8 +34,7 @@ process MMSEQS_CLUSTER {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/createdb/main.nf b/modules/nf-core/mmseqs/createdb/main.nf
@@ -33,8 +33,7 @@ process MMSEQS_CREATEDB {
         createdb \\
         ${sequence_name} \\
         ${prefix}/${prefix} \\
-        $args \\
-        --compressed 1
+        $args
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf
@@ -30,8 +30,7 @@ process MMSEQS_CREATEINDEX {
         \${DB_INPUT_PATH_NAME} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/createtsv/main.nf b/modules/nf-core/mmseqs/createtsv/main.nf
@@ -40,8 +40,7 @@ process MMSEQS_CREATETSV {
         \$DB_RESULT_PATH_NAME \\
         ${prefix}.tsv \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf
@@ -28,7 +28,6 @@ process MMSEQS_DATABASES {
         ${prefix}/database \\
         tmp/ \\
         --threads ${task.cpus} \\
-        --compressed 1 \\
         ${args}
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/mmseqs/easysearch/main.nf b/modules/nf-core/mmseqs/easysearch/main.nf
@@ -36,8 +36,7 @@ process MMSEQS_EASYSEARCH {
         ${prefix}.tsv \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/mmseqs/linclust/main.nf b/modules/nf-core/mmseqs/linclust/main.nf
@@ -34,8 +34,7 @@ process MMSEQS_LINCLUST {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/search/main.nf b/modules/nf-core/mmseqs/search/main.nf
@@ -40,9 +40,7 @@ process MMSEQS_SEARCH {
         ${prefix}/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
-
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/mmseqs/taxonomy/main.nf b/modules/nf-core/mmseqs/taxonomy/main.nf
@@ -38,8 +38,7 @@ process MMSEQS_TAXONOMY {
         ${prefix}_taxonomy/${prefix} \\
         tmp1 \\
         $args \\
-        --threads ${task.cpus} \\
-        --compressed 1
+        --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":