snapzipsort: use ubam for alignment

conf/modules.config

@@ -249,10 +249,23 @@ process {
         }
     }
 
+    withName: '.*FGUMI_SORT' {
+        ext.prefix = { "${meta.id}.fgumi.unmapped.sorted" }
+        ext.args   = {
+            [
+                "--order queryname",
+                "--compression-level 0",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
+                "--key-types mi"
+            ].join(" ").trim()
+        }
+    }
+
     //// FGUMI fastq | SNAP | zipper (step 3a)
     withName: RAW_FGUMI_SNAPZIPSORT {
         ext.prefix = { "${meta.id}.fgumi" }
-        ext.args2  = {
+        ext.args  = {
             [
                 "-b-",
                 "-sm 20",
@@ -264,35 +277,52 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
+        ext.args2  = {
+            [
+                "--order queryname",
+                "--compression-level 0",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
+                "--key-types mi"
+            ].join(" ").trim()
+        }
         ext.args4  = {
             [
                 "--order template-coordinate",
-                "--max-memory ${task.memory.toGiga()}G",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--key-types mi",
+                "--tmp-dir .",
             ].join(" ").trim()
         }
     }
 
     //// FGUMI group (step 4)
     withName: '.*FGUMI_GROUP' {
         ext.prefix = { "${meta.id}.fgumi.group" }
-        ext.args   = { "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" }
+        ext.args   = {
+            [
+                "--edits ${meta.fgumi_group_edits != null ? meta.fgumi_group_edits : 1}" ,
+                "--max-memory ${task.memory.toGiga() / task.cpus}G"
+            ].join(" ").trim()
+        }
     }
 
     //// FGUMI simplex (step 5)
     withName: '.*FGUMI_SIMPLEX' {
         ext.prefix = { "${meta.id}.fgumi.simplex" }
-        ext.args   = { "--max-memory ${task.memory.toGiga()}G" }
+        ext.args   = { "--max-memory ${task.memory.toGiga() / task.cpus}G" }
     }
 
     //// FGUMI filter + coordinate sort/index (step 7)
     withName: '.*FGUMI_FILTER' {
         ext.prefix = { "${meta.id}.fgumi.filter" }
+        ext.args   = { "--max-memory ${task.memory.toGiga() / task.cpus}G" }
     }
 
     //// FGUMI consensus alignment (step 8)
     withName: UMI_FGUMI_SNAPZIPSORT {
         ext.prefix = { "${meta.id}.fgumi" }
-        ext.args2  = {
+        ext.args  = {
             [
                 "-b-",
                 "-sm 20",
@@ -304,10 +334,19 @@ process {
                 meta.readgroup ? "-R \"@RG\\t" + meta.readgroup.findResults { rg -> rg.value?.trim() ? "${rg.key}:${rg.value}" : null }.join("\\t") + "\"" : "",
             ].join(" ").trim()
         }
+        ext.args2  = {
+            [
+                "--order queryname",
+                "--compression-level 0",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
+                "--tmp-dir .",
+                "--key-types mi"
+            ].join(" ").trim()
+        }
         ext.args4  = {
             [
                 "--order coordinate",
-                "--max-memory ${task.memory.toGiga()}G",
+                "--max-memory ${task.memory.toGiga() / task.cpus}G",
                 "--write-index",
             ].join(" ").trim()
         }

modules.json

@@ -77,6 +77,11 @@
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/fgumi/simplex/fgumi-simplex.diff"
                     },
+                    "fgumi/sort": {
+                        "branch": "master",
+                        "git_sha": "c3e04783b2ac99ffc011745ec092614a7bef86ca",
+                        "installed_by": ["modules"]
+                    },
                     "gnu/sort": {
                         "branch": "master",
                         "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120",

modules/local/fgumi/snapzipsort/main.nf

@@ -32,16 +32,20 @@ process FGUMI_SNAPZIPSORT {
     [ -z "\$INDEX_FILE" ] && echo "Snap index files not found" 1>&2 && exit 1
     INDEX=\$(dirname "\$INDEX_FILE")
 
-    fgumi fastq \\
-        --input ${unmapped_bam} \\
-        ${args} \\
-    | snap-aligner paired \\
+    snap-aligner paired \\
         \$INDEX \\
-        -pairedInterleavedFastq - \\
+        ${unmapped_bam} \\
         -t ${task.cpus} \\
         -o -bam - \\
-        ${args2} \\
-    | fgumi zipper \\
+        ${args} \\
+    | fgumi sort \\
+        --input - \\
+        --output ${prefix}.intermediate.bam \\
+        --threads ${task.cpus} \\
+        ${args2}
+
+    fgumi zipper \\
+        --input ${prefix}.intermediate.bam \\
         --unmapped ${unmapped_bam} \\
         --reference ${fasta} \\
         --threads ${task.cpus} \\