mirpedrol · mirpedrol · Nov 27, 2024 · Nov 27, 2024 · Nov 27, 2024 · Nov 27, 2024
diff --git a/assets/schema_evaluate.json b/assets/schema_evaluate.json
@@ -46,9 +46,9 @@
             "msa": {
                 "type": "string",
                 "format": "file-path",
-                "pattern": "^\\S+\\.aln$",
+                "pattern": "^\\S+\\.aln(\\.gz)?$",
                 "description": "aln file containing the MSA",
-                "errorMessage": "Must end with .aln",
+                "errorMessage": "Must end with .aln or .aln.gz",
                 "meta": ["msa"]
             },
             "reference": {

diff --git a/modules.json b/modules.json
@@ -13,7 +13,7 @@
                     "clustalo/guidetree": {
                         "branch": "main",
                         "git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
-                        "installed_by": ["msa_guidetree"]
+                        "installed_by": ["modules", "msa_guidetree"]
                     },
                     "clustalo/treealign": {
                         "branch": "main",
@@ -37,7 +37,7 @@
                     },
                     "kalign/align": {
                         "branch": "main",
-                        "git_sha": "caf37f3ee943a8101000b25ba502f038f8bfeb87",
+                        "git_sha": "34e891b859086dd03e52e79abcf47b3863fcb3cb",
                         "installed_by": ["msa_alignment"]
                     },
                     "learnmsa/align": {
@@ -47,7 +47,7 @@
                     },
                     "mafft": {
                         "branch": "main",
-                        "git_sha": "caf37f3ee943a8101000b25ba502f038f8bfeb87",
+                        "git_sha": "34e891b859086dd03e52e79abcf47b3863fcb3cb",
                         "installed_by": ["msa_alignment"]
                     },
                     "magus/align": {
@@ -57,7 +57,7 @@
                     },
                     "magus/guidetree": {
                         "branch": "main",
-                        "git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
+                        "git_sha": "519be3b194f5e2e271436398c1646c538867fe3e",
                         "installed_by": ["msa_guidetree"]
                     },
                     "magus/treealign": {
@@ -67,7 +67,7 @@
                     },
                     "muscle5/super5": {
                         "branch": "main",
-                        "git_sha": "1ecfdd11db17d75ba0499992d8d0a3222885645e",
+                        "git_sha": "34e891b859086dd03e52e79abcf47b3863fcb3cb",
                         "installed_by": ["msa_alignment"]
                     },
                     "tcoffee/align": {
@@ -107,48 +107,48 @@
                 "nf-core": {
                     "csvtk/concat": {
                         "branch": "master",
-                        "git_sha": "cfe2a24902bfdfe8132f11461ffda92d257f9f09",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "csvtk/join": {
                         "branch": "master",
-                        "git_sha": "614abbf126f287a3068dc86997b2e1b6a93abe20",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/csvtk/join/csvtk-join.diff"
                     },
                     "pigz/compress": {
                         "branch": "master",
-                        "git_sha": "0eab94fc1e48703c1b0a8704bd665f554905c39d",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "pigz/uncompress": {
                         "branch": "master",
-                        "git_sha": "d7f0de8aae7bf84b080dfdcf4e294bf11a46a51c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/alncompare": {
                         "branch": "master",
-                        "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59",
+                        "git_sha": "ffa000ab3c33df25a165b5f9a039c4cbb665a77b",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/irmsd": {
                         "branch": "master",
-                        "git_sha": "faf557ba56156ac0e5de76a25c1e3df11c944f59",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/seqreformat": {
                         "branch": "master",
-                        "git_sha": "32ae618a60a25a870b5fa47ea2060ddcd911ab53",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tcoffee/tcs": {
                         "branch": "master",
-                        "git_sha": "1cacaceabae75b0c3bc393dee52cb6a5020fcb5c",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/mirpedrol/clustalo/align/main.nf b/modules/mirpedrol/clustalo/align/main.nf
@@ -11,7 +11,7 @@ process CLUSTALO_ALIGN {
     tuple val(meta) , path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -30,7 +30,7 @@ process CLUSTALO_ALIGN {
         -i ${fasta} \
         --threads=${task.cpus} \
         $args \
-        > ${prefix}.aln
+        --force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -43,7 +43,7 @@ process CLUSTALO_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/clustalo/treealign/main.nf b/modules/mirpedrol/clustalo/treealign/main.nf
@@ -12,7 +12,7 @@ process CLUSTALO_TREEALIGN {
     tuple val(meta2), path(tree)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -32,7 +32,7 @@ process CLUSTALO_TREEALIGN {
         --guidetree-in=${tree} \
         --threads=${task.cpus} \
         $args \
-        > ${prefix}.aln
+        --force -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -45,7 +45,7 @@ process CLUSTALO_TREEALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/famsa/align/main.nf b/modules/mirpedrol/famsa/align/main.nf
@@ -13,7 +13,7 @@ process FAMSA_ALIGN {
     tuple val(meta) , path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -23,11 +23,11 @@ process FAMSA_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    famsa \\
+    famsa -gz \\
         $args \\
         -t ${task.cpus} \\
         ${fasta} \\
-        ${prefix}.aln
+        ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +38,7 @@ process FAMSA_ALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/famsa/treealign/main.nf b/modules/mirpedrol/famsa/treealign/main.nf
@@ -14,7 +14,7 @@ process FAMSA_TREEALIGN {
     tuple val(meta2), path(tree)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -24,12 +24,12 @@ process FAMSA_TREEALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    famsa import $tree \\
+    famsa -gt import $tree \\
         -gz \\
         $args \\
         -t ${task.cpus} \\
         ${fasta} \\
-        ${prefix}.aln
+        ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -40,7 +40,7 @@ process FAMSA_TREEALIGN {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/kalign/align/main.nf b/modules/mirpedrol/kalign/align/main.nf
@@ -11,7 +11,7 @@ process KALIGN_ALIGN {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -24,7 +24,7 @@ process KALIGN_ALIGN {
     unpigz -cdf $fasta | \\
     kalign \\
         $args \\
-        -o ${prefix}.aln
+        -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,7 +37,7 @@ process KALIGN_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/kalign/align/tests/main.nf.test b/modules/mirpedrol/kalign/align/tests/main.nf.test
@@ -26,7 +26,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta")},
+                { assert snapshot(process.out.alignment).match("alignment")},
+                { assert snapshot(process.out.versions).match("versions")}
             )
         }
     }

diff --git a/modules/mirpedrol/learnmsa/align/main.nf b/modules/mirpedrol/learnmsa/align/main.nf
@@ -11,7 +11,7 @@ process LEARNMSA_ALIGN {
     tuple val(meta), path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -24,7 +24,7 @@ process LEARNMSA_ALIGN {
     learnMSA \\
         $args \\
         -i <(unpigz -cdf $fasta) \\
-        -o ${prefix}.aln
+        -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -37,7 +37,7 @@ process LEARNMSA_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/mafft/main.nf b/modules/mirpedrol/mafft/main.nf
@@ -11,7 +11,7 @@ process MAFFT {
     tuple val(meta) , path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -25,7 +25,7 @@ process MAFFT {
         --thread ${task.cpus} \\
         ${args} \\
         ${fasta} \\
-        > ${prefix}.aln
+        | pigz -cp ${task.cpus} > ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -38,7 +38,7 @@ process MAFFT {
     def args         = task.ext.args   ?: ''
     def prefix       = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    touch ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/mafft/tests/main.nf.test b/modules/mirpedrol/mafft/tests/main.nf.test
@@ -23,7 +23,8 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match("SARS-CoV-2 scaffolds fasta")}
+                { assert snapshot(process.out.alignment).match("alignment")},
+                { assert snapshot(process.out.versions).match("mafft_versions")}
             )
         }
 

diff --git a/modules/mirpedrol/magus/align/main.nf b/modules/mirpedrol/magus/align/main.nf
@@ -11,7 +11,7 @@ process MAGUS_ALIGN {
     tuple val(meta) , path(fasta)
 
     output:
-    tuple val(meta), path("*.aln"), emit: alignment
+    tuple val(meta), path("*.aln.gz"), emit: alignment
     path "versions.yml"              , emit: versions
 
     when:
@@ -28,7 +28,7 @@ process MAGUS_ALIGN {
         -np $task.cpus \\
         -i $fasta \\
         -d ./ \\
-        -o ${prefix}.aln \\
+        --overwrite -o >(pigz -cp ${task.cpus} > ${prefix}.aln.gz) \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -42,7 +42,7 @@ process MAGUS_ALIGN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.aln
+    echo "" | gzip > ${prefix}.aln.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/mirpedrol/magus/guidetree/meta.yml b/modules/mirpedrol/magus/guidetree/meta.yml
@@ -28,7 +28,7 @@ input:
     - fasta:
         type: file
         description: Input sequences in FASTA format.
-        pattern: "*.{fa,fna,fasta}"
+        pattern: "*.{fa,fasta}"
         ontologies:
           - edam: http://edamontology.org/format_1929
 output:
@@ -41,7 +41,7 @@ output:
       - "*.dnd":
           type: file
           description: File containing the output guidetree, in newick format.
-          pattern: "*.dnd"
+          pattern: "*.{dnd}"
   - versions:
       - versions.yml:
           type: file