Update metamdbg version; use gzipped bin files

sanger-tol · Dec 18, 2024 · 9950440 · 9950440
1 parent 4cac07b
commit 9950440
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Showing 28 changed files with 681 additions and 94 deletions.
diff --git a/bin/bin_summary.R b/bin/bin_summary.R
@@ -103,6 +103,9 @@ read_taxonomy <- function(file) {
             ncbi_classification = `Majority vote NCBI classification`,
             taxid)
     }
+    # gtdb doesn't drop the extension
+    df <- df |>
+        mutate(bin = str_extract(bin, "(.*)\\.[^\\.]+$", group = 1))
 
     return(df)
 }

diff --git a/conf/modules.config b/conf/modules.config
@@ -55,7 +55,7 @@ process {
     }
 
     withName: 'CHECKM2_PREDICT' {
-        ext.args   = { "--extension fa" }
+        ext.args   = { "--extension gz" }
         ext.prefix = { "${meta.id}_${meta.assembler}_${meta.binner}" }
         tag        = { "${meta.id}_${meta.assembler}_${meta.binner}" }
         publishDir = [
@@ -134,7 +134,7 @@ process {
     }
 
     withName: 'GTDBTK_CLASSIFYWF' {
-        ext.args   = "--extension fa"
+        ext.args   = "--extension gz"
         ext.prefix = { "${meta.id}_${meta.assembler}_${meta.binner}" }
         tag        = { "${meta.id}_${meta.assembler}_${meta.binner}" }
         publishDir = [

diff --git a/modules.json b/modules.json
@@ -5,6 +5,11 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
+                    "barrnap": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bwamem2/index": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -57,8 +62,7 @@
                     "maxbin2": {
                         "branch": "master",
                         "git_sha": "283613159e079152f1336cef0db1c836086206e0",
-                        "installed_by": ["modules"],
-                        "patch": "modules/nf-core/maxbin2/maxbin2.diff"
+                        "installed_by": ["modules"]
                     },
                     "metabat2/metabat2": {
                         "branch": "master",
@@ -68,7 +72,7 @@
                     },
                     "metamdbg/asm": {
                         "branch": "master",
-                        "git_sha": "7c08494acb5aba0763c5c6db87f82b249de87ea8",
+                        "git_sha": "88fbcaa0e08c4f5ab925bebe2234b2b68953e8cd",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
@@ -82,6 +86,11 @@
                         "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
+                    "prokka": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "pyrodigal": {
                         "branch": "master",
                         "git_sha": "938e803109104e30773f76a7142442722498fef1",

diff --git a/modules/local/bin3c/cluster/main.nf b/modules/local/bin3c/cluster/main.nf
@@ -7,7 +7,7 @@ process BIN3C_CLUSTER {
     tuple val(meta), path(contigs), path(map)
 
     output:
-    tuple val(meta), path("*.fa")         , emit: fasta, optional: true
+    tuple val(meta), path("*.fa.gz")      , emit: fasta, optional: true
     tuple val(meta), path("*.[!fna,log]*"), emit: clustering
     tuple val(meta), path("*.log")        , emit: log
     path("versions.yml")                  , emit: versions
@@ -27,11 +27,12 @@ process BIN3C_CLUSTER {
 
     # bin3c renames contigs, we don't want that
     for bin in bin3c/fasta/*.fna; do
-        basename=`basename \$bin`
-        awk -F" " '{if(\$1~">"){print ">" substr(\$2,8)}else{print \$0}}' \$bin > ${prefix}.\${basename%.fna}.fa
+        bn=`basename \$bin .fna`
+        awk -F" " '{if(\$1~">"){print ">" substr(\$2,8)}else{print \$0}}' \$bin > ${prefix}.\${bn}.fa
     done
 
     find bin3c -maxdepth 1 -type f -exec sh -c 'name=`basename {}`; mv {} ${prefix}.\$name' \\;
+    gzip *.fa
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/contig2bintofasta/main.nf b/modules/local/contig2bintofasta/main.nf
@@ -11,8 +11,8 @@ process CONTIG2BINTOFASTA {
     tuple val(meta), path(contigs), path(contig2bin)
 
     output:
-    tuple val(meta), path("*.fa*"), emit: bins
-    path("versions.yml")          , emit: versions
+    tuple val(meta), path("*.fa.gz"), emit: bins
+    path("versions.yml")            , emit: versions
 
     script:
     def args        = task.ext.args   ?: ''
@@ -21,7 +21,7 @@ process CONTIG2BINTOFASTA {
     awk '{print \$2}' ${contig2bin} | sort -u | while read bin
     do
         grep -w \${bin} ${contig2bin} | awk '{ print \$1 }' > \${bin}.ctglst
-        seqkit grep -f \${bin}.ctglst ${contigs} > \${bin}.fa
+        seqkit grep -f \${bin}.ctglst ${contigs} | gzip > \${bin}.fa.gz
     done
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/local/fastatocontig2bin/main.nf b/modules/local/fastatocontig2bin/main.nf
@@ -16,19 +16,28 @@ process FASTATOCONTIG2BIN {
     path("versions.yml")          , emit: versions
 
     script:
-    def args        = task.ext.args   ?: ''
-    def prefix      = task.ext.prefix ?: "${meta.id}"
+    def args              = task.ext.args   ?: ''
+    def prefix            = task.ext.prefix ?: "${meta.id}"
+    def compressed_bins   = bins.findAll { it.getExtension() == "gz" }
+    def decompress_bins   = compressed_bins.size() > 0 ? "gunzip ${compressed_bins.join(" ")}" : ""
+    def clean_bins        = bins.collect { it.toString() - ~/\.gz$/ }
+    def remove_compressed = compressed_bins.size() > 0 ? "rm ${compressed_bins.collect { it.toString() - ~/\.gz$/ }.join(" ")}" : ""
     """
+    ${decompress_bins}
+
     awk \\
         'BEGIN { OFS = "\t" }
         BEGINFILE {
-            cmd=sprintf("basename %s .%s", FILENAME, "${extension}")
-            cmd | getline bin
+            bin = FILENAME
+            sub(".*/", "", bin)
+            sub(/\\.[^\\.]+\$/, "", bin)
         }
         /^>/ {
             sub(/>/, "", \$1)
-            print \$1,bin
-        }' ${bins} > ${prefix}.tsv
+            print \$1, bin
+        }' ${clean_bins.join(" ")} > ${prefix}.tsv
+
+    ${remove_compressed}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/local/metator/pipeline/main.nf b/modules/local/metator/pipeline/main.nf
@@ -10,10 +10,10 @@ process METATOR_PIPELINE {
     val hic_enzymes
 
     output:
-    tuple val(meta), path("bin_summary.txt")          , emit: bin_summary
-    tuple val(meta), path("binning.txt")              , emit: contig2bin
-    tuple val(meta), path("bins/*.fa"), emit: bins
-    path "versions.yml"                               , emit: versions
+    tuple val(meta), path("bin_summary.txt") , emit: bin_summary
+    tuple val(meta), path("binning.txt")     , emit: contig2bin
+    tuple val(meta), path("bins/*.fa.gz")    , emit: bins
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,6 +46,8 @@ process METATOR_PIPELINE {
         awk -F" " '{if(\$1~">"){ print \$1 } else { print \$0 } }' \$bin > bins/\${binname}
     done
 
+    gzip bins/*.fa
+
     rm -r final_bin_unscaffold
 
     cat <<-END_VERSIONS > versions.yml

diff --git a/modules/nf-core/barrnap/environment.yml b/modules/nf-core/barrnap/environment.yml
diff --git a/modules/nf-core/barrnap/main.nf b/modules/nf-core/barrnap/main.nf
diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml
diff --git a/modules/nf-core/barrnap/tests/main.nf.test b/modules/nf-core/barrnap/tests/main.nf.test