Update ampcombi 2.0.1

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

@@ -13,6 +13,7 @@ process AMPCOMBI2_PARSETABLES {
     path gbk_input
     val opt_amp_db
     path opt_amp_db_dir
+    path opt_interproscan
 
     output:
     tuple val(meta), path("${meta.id}/")                                , emit: sample_dir
@@ -34,14 +35,18 @@ process AMPCOMBI2_PARSETABLES {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    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("' '")}' \\
     --faa ${faa_input} \\
     --gbk ${gbk_input} \\
     --sample_list ${prefix} \\
     --amp_database ${opt_amp_db} \\
-    --amp_database_dir ${opt_amp_db_dir} \\
+    ${db_dir} \\
+    ${interpro} \\
     ${args} \\
     --threads ${task.cpus}
 
@@ -54,6 +59,9 @@ process AMPCOMBI2_PARSETABLES {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    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

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

@@ -17,6 +17,7 @@ keywords:
   - amptransformer
   - DRAMP
   - MMseqs2
+  - InterProScan
 tools:
   - ampcombi2/parsetables:
       description: "A parsing tool to convert and summarise the outputs from multiple
@@ -60,6 +61,10 @@ input:
         type: directory
         description: The path to the folder containing the fasta and tsv database files.
         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:

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

@@ -30,6 +30,7 @@ nextflow_process {
                 input[2] = gbk_input
                 input[3] = 'DRAMP'
                 input[4] = []
+                input[5] = []
                 """
             }
         }
@@ -72,6 +73,7 @@ nextflow_process {
                 input[2] = gbk_input
                 input[3] = 'DRAMP'
                 input[4] = []
+                input[5] = []
                 """
             }
         }

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

@@ -20,7 +20,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-05T13:02:52.664971407"
+        "timestamp": "2024-12-11T13:58:57.988191067"
     },
     "ampcombi2_parsetables - metagenome - stub": {
         "content": [

modules/nf-core/ampcombi2/parsetables/tests/nextflow.config

@@ -12,7 +12,8 @@ process {
         "--hmmsearch_file 'candidates.txt'",
         "--ampgram_file '.tsv'",
         "--amptransformer_file '.txt'",
-        "--log true"
+        "--log true",
+        "--interproscan_filter 'nonsense'"
     ].join(' ')
 
     ext.prefix = "sample_1"