Fix ampcombi (#2756)

Remove directory flag, not needed in nf-core

modules/nf-core/ampcombi/main.nf

@@ -33,12 +33,11 @@ process AMPCOMBI {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def db = opt_amp_db? "--amp_database $opt_amp_db": ""
-    def fileoption = amp_input instanceof List ? "--path_list '${amp_input.collect{"$it"}.join("' '")}'" : "--amp_results $amp_input/"
     def faa = faa_input.isDirectory() ? "--faa ${faa_input}/" : "--faa ${faa_input}"
     """
     ampcombi \\
         $args \\
-        ${fileoption} \\
+        --path_list '${amp_input.collect{"$it"}.join("' '")}' \\
         --sample_list ${prefix} \\
         --log True \\
         --threads ${task.cpus} \\

tests/modules/nf-core/ampcombi/main.nf

@@ -3,23 +3,6 @@
 nextflow.enable.dsl = 2
 
 include { AMPCOMBI } from '../../../../modules/nf-core/ampcombi/main.nf'
-include { UNTAR as UNTAR1 ; UNTAR as UNTAR2 } from '../../../../modules/nf-core/untar/main.nf'
-
-workflow test_ampcombi_directory {
-   amp_input = [
-       [ id:'sample_1'],
-       file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/ampcombi/test_files.tar.gz", checkIfExists: true)
-   ]
-   faa_input = [
-       [ id:[]],
-       file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/ampcombi/test_faa.tar.gz", checkIfExists: true)
-   ]
-   db = params.db ? file( params.db ) : []
-
-   UNTAR1 ( amp_input )
-   UNTAR2 ( faa_input )
-   AMPCOMBI ( UNTAR1.out.untar, UNTAR2.out.untar.map{ it[1] }, db )
-}
 
 workflow test_ampcombi_file_paths {
     amp_input = [[id:'sample_1'],

tests/modules/nf-core/ampcombi/test.yml

@@ -1,17 +1,3 @@
-- name: ampcombi test_ampcombi_directory
-  command: nextflow run ./tests/modules/nf-core/ampcombi -entry test_ampcombi_directory -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ampcombi/nextflow.config
-  tags:
-    - ampcombi
-  files:
-    - path: output/ampcombi/ampcombi.log
-      contains: ["found", "AMPcombi"]
-    - path: output/ampcombi/sample_1/sample_1_amp.faa
-      md5sum: 8fef1e243eed8d605b9d40082b37a703
-    - path: output/ampcombi/sample_1/sample_1_ampcombi.csv
-      contains: ["DRAMP"]
-    - path: output/ampcombi/sample_1/sample_1_diamond_matches.txt
-      contains: ["target_id"]
-
 - name: ampcombi test_ampcombi_file_paths
   command: nextflow run ./tests/modules/nf-core/ampcombi -entry test_ampcombi_file_paths -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ampcombi/nextflow.config
   tags: