Merge pull request #149 from JoseEspinosa/dev

Update modules to last version
nf-core · Apr 24, 2024 · 788bbfc · 788bbfc
2 parents df3400f + acdadb7
commit 788bbfc
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Showing 31 changed files with 569 additions and 67 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#115](https://github.com/nf-core/proteinfold/issues/115)] - Throw message error when profile conda is used.
 - [[#131](https://github.com/nf-core/proteinfold/issues/131)] - Add esmfold small tests.
 - [[#144](https://github.com/nf-core/proteinfold/issues/144)] - Force value channels when providing dbs (downloaded) in `main.nf` to enable the processing of multiple samples.
+- [[#147](https://github.com/nf-core/proteinfold/issues/147)] - Update modules to last version.
 
 ## 1.0.0 - White Silver Reebok
 

diff --git a/conf/modules_colabfold.config b/conf/modules_colabfold.config
@@ -37,7 +37,8 @@ if (params.colabfold_server == 'local') {
             ]
         }
         withName: 'MMSEQS_CREATEINDEX' {
-            ext.args = '--remove-tmp-files 1'
+            ext.args  = '--remove-tmp-files 1'
+            ext.args2 = '*_seq.tsv'
             publishDir = [
                 enabled: false
             ]

diff --git a/main.nf b/main.nf
@@ -100,16 +100,16 @@ workflow NFCORE_PROTEINFOLD {
             params.full_dbs,
             params.alphafold2_mode,
             params.alphafold2_model_preset,
-            PREPARE_ALPHAFOLD2_DBS.out.params.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]).first(),
-            PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]).first(),
-            PREPARE_ALPHAFOLD2_DBS.out.mgnify.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.pdb70.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.uniref30.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.uniref90.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres.first(),
-            PREPARE_ALPHAFOLD2_DBS.out.uniprot.first()
+            PREPARE_ALPHAFOLD2_DBS.out.params,
+            PREPARE_ALPHAFOLD2_DBS.out.bfd.ifEmpty([]),
+            PREPARE_ALPHAFOLD2_DBS.out.small_bfd.ifEmpty([]),
+            PREPARE_ALPHAFOLD2_DBS.out.mgnify,
+            PREPARE_ALPHAFOLD2_DBS.out.pdb70,
+            PREPARE_ALPHAFOLD2_DBS.out.pdb_mmcif,
+            PREPARE_ALPHAFOLD2_DBS.out.uniref30,
+            PREPARE_ALPHAFOLD2_DBS.out.uniref90,
+            PREPARE_ALPHAFOLD2_DBS.out.pdb_seqres,
+            PREPARE_ALPHAFOLD2_DBS.out.uniprot
         )
         ch_multiqc  = ALPHAFOLD2.out.multiqc_report
         ch_versions = ch_versions.mix(ALPHAFOLD2.out.versions)
@@ -141,9 +141,9 @@ workflow NFCORE_PROTEINFOLD {
         COLABFOLD (
             ch_versions,
             params.colabfold_model_preset,
-            PREPARE_COLABFOLD_DBS.out.params.first(),
-            PREPARE_COLABFOLD_DBS.out.colabfold_db.first(),
-            PREPARE_COLABFOLD_DBS.out.uniref30.first(),
+            PREPARE_COLABFOLD_DBS.out.params,
+            PREPARE_COLABFOLD_DBS.out.colabfold_db,
+            PREPARE_COLABFOLD_DBS.out.uniref30,
             params.num_recycle
         )
         ch_multiqc  = COLABFOLD.out.multiqc_report

diff --git a/modules.json b/modules.json
@@ -7,8 +7,9 @@
                 "nf-core": {
                     "aria2": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "git_sha": "7d0ccc097c60d23a195099b326a5882e135c7949",
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/aria2/aria2.diff"
                     },
                     "gunzip": {
                         "branch": "master",
@@ -17,12 +18,12 @@
                     },
                     "mmseqs/createindex": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3",
                         "installed_by": ["modules"]
                     },
                     "mmseqs/tsv2exprofiledb": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -32,7 +33,7 @@
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
+                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/untar/untar.diff"
                     }

diff --git a/modules/nf-core/aria2/aria2.diff b/modules/nf-core/aria2/aria2.diff
diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml
diff --git a/modules/nf-core/aria2/main.nf b/modules/nf-core/aria2/main.nf
diff --git a/modules/nf-core/aria2/meta.yml b/modules/nf-core/aria2/meta.yml
diff --git a/modules/nf-core/aria2/tests/main.nf.test b/modules/nf-core/aria2/tests/main.nf.test
diff --git a/modules/nf-core/aria2/tests/main.nf.test.snap b/modules/nf-core/aria2/tests/main.nf.test.snap
diff --git a/modules/nf-core/aria2/tests/tags.yml b/modules/nf-core/aria2/tests/tags.yml
diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml
diff --git a/modules/nf-core/mmseqs/createindex/main.nf b/modules/nf-core/mmseqs/createindex/main.nf