Update ampcombi 2.0.1

modules/nf-core/ampcombi2/cluster/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"

modules/nf-core/ampcombi2/cluster/main.nf

@@ -4,8 +4,8 @@ process AMPCOMBI2_CLUSTER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summary_file)

modules/nf-core/ampcombi2/cluster/tests/main.nf.test.snap

@@ -4,14 +4,14 @@
             true,
             true,
             [
-                "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                "versions.yml:md5,b629089d44775078dce5e664a455422b"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:11:40.928513749"
+        "timestamp": "2024-12-03T07:57:01.869983435"
     },
     "ampcombi2_cluster - metagenome - stub": {
         "content": [
@@ -26,7 +26,7 @@
                     "Ampcombi_cluster.log:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "3": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ],
                 "cluster_tsv": [
                     "Ampcombi_summary_cluster.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
@@ -38,14 +38,14 @@
                     "Ampcombi_summary_cluster_representative_seq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,4e9aa3812bfee6ec22a1b6ccb62de2ca"
+                    "versions.yml:md5,b629089d44775078dce5e664a455422b"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-24T12:12:08.780718892"
+        "timestamp": "2024-12-03T07:57:23.939137628"
     }
 }

modules/nf-core/ampcombi2/complete/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"

modules/nf-core/ampcombi2/complete/main.nf

@@ -4,8 +4,8 @@ process AMPCOMBI2_COMPLETE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     path(summaries)

modules/nf-core/ampcombi2/complete/tests/main.nf.test.snap

@@ -6,39 +6,39 @@
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "1": [
-                    
+
                 ],
                 "2": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ],
                 "log": [
-                    
+
                 ],
                 "tsv": [
                     "Ampcombi_summary.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "versions": [
-                    "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                    "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:55:16.030399422"
+        "timestamp": "2024-12-03T07:57:53.385349848"
     },
     "ampcombi2_complete - contigs": {
         "content": [
             true,
             [
-                "versions.yml:md5,0aa35e86761a6c160482b8b8dbfc5440"
+                "versions.yml:md5,bfba0046e0cfa7b0b6d79663823f94c0"
             ]
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-04-29T11:54:54.334224301"
+        "timestamp": "2024-12-03T07:57:40.263912946"
     }
-}
+}

modules/nf-core/ampcombi2/parsetables/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - "bioconda::ampcombi=0.2.2"
+  - "bioconda::ampcombi=2.0.1"

modules/nf-core/ampcombi2/parsetables/main.nf

@@ -1,47 +1,53 @@
 process AMPCOMBI2_PARSETABLES {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ampcombi:0.2.2--pyhdfd78af_0':
-        'biocontainers/ampcombi:0.2.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/ampcombi:2.0.1--pyhdfd78af_0':
+        'biocontainers/ampcombi:2.0.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(amp_input)
-    path(faa_input)
-    path(gbk_input)
-    path(opt_amp_db)
+    path faa_input
+    path gbk_input
+    val opt_amp_db
+    path opt_amp_db_dir
+    path opt_interproscan
 
     output:
-    tuple val(meta), path("${meta.id}/")                              , emit: sample_dir
-    tuple val(meta), path("${meta.id}/contig_gbks/")                  , emit: contig_gbks
-    tuple val(meta), path("${meta.id}/${meta.id}_diamond_matches.txt"), emit: txt
-    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv")       , emit: tsv
-    tuple val(meta), path("${meta.id}/${meta.id}_amp.faa")            , emit: faa
-    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log")       , emit: sample_log, optional:true
-    tuple val(meta), path("Ampcombi_parse_tables.log")                , emit: full_log, optional:true
-    tuple val(meta), path("amp_ref_database/")                        , emit: results_db, optional:true
-    tuple val(meta), path("amp_ref_database/*.dmnd")                  , emit: results_db_dmnd, optional:true
-    tuple val(meta), path("amp_ref_database/*.clean.fasta")           , emit: results_db_fasta, optional:true
-    tuple val(meta), path("amp_ref_database/*.tsv")                   , emit: results_db_tsv, optional:true
-    path "versions.yml"                                               , emit: versions
+    tuple val(meta), path("${meta.id}/")                                , emit: sample_dir
+    tuple val(meta), path("${meta.id}/contig_gbks/")                    , emit: contig_gbks
+    tuple val(meta), path("${meta.id}/${meta.id}_mmseqs_matches.tsv")   , emit: db_tsv
+    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.tsv")         , emit: tsv
+    tuple val(meta), path("${meta.id}/${meta.id}_amp.faa")              , emit: faa
+    tuple val(meta), path("${meta.id}/${meta.id}_ampcombi.log")         , emit: sample_log   , optional:true
+    tuple val(meta), path("Ampcombi_parse_tables.log")                  , emit: full_log     , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/")                , emit: db           , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/*.txt")           , emit: db_txt       , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/*.fasta")         , emit: db_fasta     , optional:true
+    tuple val(meta), path("amp_${opt_amp_db}_database/mmseqs2/")        , emit: db_mmseqs    , optional:true
+    path "versions.yml"                                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def db = opt_amp_db? "--amp_database $opt_amp_db": ""
+    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
+    def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
+
     """
     ampcombi parse_tables \\
-    --path_list '${amp_input.collect{"$it"}.join("' '")}' \\
+    --path_list '${amp_input.collect { "${it}" }.join("' '")}' \\
     --faa ${faa_input} \\
     --gbk ${gbk_input} \\
     --sample_list ${prefix} \\
-    ${db} \\
-    $args \\
+    --amp_database ${opt_amp_db} \\
+    ${db_dir} \\
+    ${interpro} \\
+    ${args} \\
     --threads ${task.cpus}
 
     cat <<-END_VERSIONS > versions.yml
@@ -53,20 +59,30 @@ process AMPCOMBI2_PARSETABLES {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def db = opt_amp_db? "--amp_database $opt_amp_db": ""
+    def db_dir = opt_amp_db_dir ? "--amp_database_dir ${opt_amp_db_dir}" : ""
+    def interpro = opt_interproscan ? "--interproscan_output ${opt_interproscan}" : ""
+
     """
     mkdir -p ${prefix}
     mkdir -p ${prefix}/contig_gbks
-    touch ${prefix}/${meta.id}_diamond_matches.txt
+    touch ${prefix}/${meta.id}_mmseqs_matches.tsv
     touch ${prefix}/${meta.id}_ampcombi.tsv
     touch ${prefix}/${meta.id}_amp.faa
     touch ${prefix}/${meta.id}_ampcombi.log
     touch Ampcombi_parse_tables.log
 
-    mkdir -p amp_ref_database
-    touch amp_ref_database/*.dmnd
-    touch amp_ref_database/*.clean.fasta
-    touch amp_ref_database/*.tsv
+    mkdir -p amp_${opt_amp_db}_database
+    mkdir -p amp_${opt_amp_db}_database/mmseqs2
+    touch amp_${opt_amp_db}_database/*.fasta
+    touch amp_${opt_amp_db}_database/*.txt
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.dbtype
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.dbtype
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB_h.index
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.index
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.lookup
+    touch amp_${opt_amp_db}_database/mmseqs2/ref_DB.source
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/ampcombi2/parsetables/meta.yml

@@ -16,12 +16,14 @@ keywords:
   - ampgram
   - amptransformer
   - DRAMP
+  - MMseqs2
+  - InterProScan
 tools:
   - ampcombi2/parsetables:
       description: "A parsing tool to convert and summarise the outputs from multiple
         AMP detection tools in a standardized format."
       homepage: "https://github.com/Darcy220606/AMPcombi"
-      documentation: "https://github.com/Darcy220606/AMPcombi"
+      documentation: "https://ampcombi.readthedocs.io/en/main/"
       tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev"
       licence: ["MIT"]
       identifier: ""
@@ -52,9 +54,17 @@ input:
           name.
         pattern: "*.gbk"
   - - opt_amp_db:
+        type: string
+        description: The name of the database to download and set up. This can either be 'DRAMP', 'APD' or 'UniRef100'.
+        pattern: "DRAMP|APD|UniRef100"
+  - - opt_amp_db_dir:
         type: directory
         description: The path to the folder containing the fasta and tsv database files.
-        pattern: "*/"
+        pattern: "path/to/amp_*_database"
+  - - opt_interproscan:
+        type: directory
+        description:  The path to the file corresponding to the respective tsv files containing the protein classifications of the annotated CDSs. The file must be the raw output from InterProScan and have an extension of '.tsv'.
+        pattern: "*.faa.tsv"
 output:
   - sample_dir:
       - meta:
@@ -78,17 +88,17 @@ output:
           description: The output subdirectory that contains the gbk files containing
             the AMP hits for each sample.
           pattern: "/*/contig_gbks"
-  - txt:
+  - db_tsv:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - ${meta.id}/${meta.id}_diamond_matches.txt:
+      - ${meta.id}/${meta.id}_mmseqs_matches.tsv:
           type: file
-          description: An alignment file containing the results from the DIAMOND alignment
+          description: An alignment file containing the results from the MMseqs2 alignment
             step done on all AMP hits.
-          pattern: "/*/*_diamond_matches.txt"
+          pattern: "/*/*_mmseqs_matches.tsv"
   - tsv:
       - meta:
           type: map
@@ -134,50 +144,51 @@ output:
           description: A log file that captures the standard output for the entire process
             in a log file. Can be activated by `--log`.
           pattern: "Ampcombi_parse_tables.log"
-  - results_db:
+  - db:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - amp_ref_database/:
+      - amp_${opt_amp_db}_database/:
           type: directory
-          description: If the AMP reference database is not provided by the user using
+          description: If the AMP reference database ID is not provided by the user using
             the flag `--amp_database', by default the DRAMP database will be downloaded,
             filtered and stored in this folder.
-          pattern: "/amp_ref_database"
-  - results_db_dmnd:
+          pattern: "/amp_*_database"
+  - db_txt:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - amp_ref_database/*.dmnd:
+      - amp_${opt_amp_db}_database/*.txt:
           type: file
-          description: AMP reference database converted to DIAMOND database format.
-          pattern: "/amp_ref_database/*.dmnd"
-  - results_db_fasta:
+          description: AMP reference database in tsv-format with two columns containing
+            header and sequence.
+          pattern: "/amp_*_database/*.txt"
+  - db_fasta:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - amp_ref_database/*.clean.fasta:
+      - amp_${opt_amp_db}_database/*.fasta:
           type: file
-          description: AMP reference database fasta file, cleaned of diamond-uncompatible
+          description: AMP reference database fasta file in clean format.
             characters.
-          pattern: "/amp_ref_database/*.clean.fasta"
-  - results_db_tsv:
+          pattern: "/amp_*_database/*.fasta"
+  - db_mmseqs:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. `[ id:'sample1', single_end:false ]`
-      - amp_ref_database/*.tsv:
-          type: file
-          description: AMP reference database in tsv-format with two columns containing
-            header and sequence.
-          pattern: "/amp_ref_database/*.tsv"
+      - amp_${opt_amp_db}_database/mmseqs2/:
+          type: directory
+          description: As alignment to the reference database is carried out by MMseqs2, this directory
+            contains all the files generated by MMseqs2 on the fasta file of the database.
+          pattern: "/amp_*_database/mmseqs2"
   - versions:
       - versions.yml:
           type: file