Merge pull request qbic-pipelines#7 from AntoniaSchuster/update_prodigal

Update module prodigal
AntoniaSchuster · Jan 28, 2022 · eb69b10 · eb69b10
2 parents cda8103 + 03b6f4b
commit eb69b10
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Showing 6 changed files with 35 additions and 103 deletions.
diff --git a/modules.json b/modules.json
@@ -6,14 +6,11 @@
             "custom/dumpsoftwareversions": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
-            "gunzip": {
-                "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
-            },
             "multiqc": {
                 "git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
             },
             "prodigal": {
-                "git_sha": "d473a247d2e0c619b0df877ea19d9a5a98c8e3c8"
+                "git_sha": "a45e03016632fe7dc2f48bfa73d9642c7f03e035"
             }
         }
     }

diff --git a/modules/nf-core/modules/gunzip/main.nf b/modules/nf-core/modules/gunzip/main.nf
diff --git a/modules/nf-core/modules/gunzip/meta.yml b/modules/nf-core/modules/gunzip/meta.yml
diff --git a/modules/nf-core/modules/prodigal/main.nf b/modules/nf-core/modules/prodigal/main.nf
diff --git a/modules/nf-core/modules/prodigal/meta.yml b/modules/nf-core/modules/prodigal/meta.yml
diff --git a/workflows/metapep.nf b/workflows/metapep.nf
@@ -62,7 +62,6 @@ include { INPUT_CHECK } from '../subworkflows/local/input_check'
 //
 // MODULE: Installed directly from nf-core/modules
 //
-include { GUNZIP                      } from '../modules/nf-core/modules/gunzip/main'
 include { PRODIGAL                    } from '../modules/nf-core/modules/prodigal/main'
 include { MULTIQC                     } from '../modules/nf-core/modules/multiqc/main'
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main'
@@ -225,22 +224,8 @@ workflow METAPEP {
     )
     ch_versions = ch_versions.mix(DOWNLOAD_PROTEINS.out.versions)
 
-    ch_nucl_input
-        .branch{ meta, file ->
-            zipped: file.name =~ ~/(?i)[.]gz$/
-            unzipped: true
-        }
-        .set {ch_nucl_unzip}
-
-    GUNZIP(
-        ch_nucl_unzip.zipped
-    )
-    ch_versions = ch_versions.mix(GUNZIP.out.versions)
-
-    ch_nucl_input_unzipped = GUNZIP.out.gunzip.concat(ch_nucl_unzip.unzipped)
-
     PRODIGAL(
-        ch_nucl_input_unzipped,
+        ch_nucl_input,
         "gff"
     )
     ch_versions = ch_versions.mix(PRODIGAL.out.versions)