Merge remote-tracking branch 'upstream/dev' into dev

Author: jscgh

CHANGELOG.md

@@ -43,6 +43,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[PR #315](https://github.com/nf-core/proteinfold/pull/315)] - Add global db flag.
 - [[#263](https://github.com/nf-core/proteinfold/issues/263)] - Removed broken colabfold options (`auto` and `alphafold2`)
 - [[PR #316](https://github.com/nf-core/proteinfold/pull/316)] - Add process_gpu label to modules which use GPU.
+- [[PR #319](https://github.com/nf-core/proteinfold/pull/319)] - Update boltz workflow to accept YAML as input.
 
 ### Parameters
 

workflows/boltz.nf

@@ -53,8 +53,23 @@ workflow BOLTZ {
     msa_server
 
     main:
-    ch_samplesheet.join(
-        ch_samplesheet.map{[it[0], it[1].text.findAll {letter -> letter == ">" }.size()]}
+    ch_samplesheet
+        .branch {
+            fasta: it[1].extension == "fasta" || it[1].extension == "fa"
+            yaml: it[1].extension == "yaml" || it[1].extension == "yml"
+        }
+        .set { ch_input_by_ext }
+
+    ch_input_by_ext.fasta
+        .join(
+            ch_input_by_ext.fasta
+                .map { meta, file ->
+                    [
+                        meta,
+                        file.text.findAll { letter -> letter == ">" }.size()
+                    ]
+                }
+        )
     )
     .map{
         def meta = it[0].clone()
@@ -103,9 +118,14 @@ workflow BOLTZ {
             ch_prepare_fasta
         )
 
+    ch_input_by_ext.yaml
+        .map { meta, file -> [meta, file, []] }  // already in YAML
+        .mix(BOLTZ_FASTA.out.formatted_fasta)    // newly converted from FASTA
+        .set { ch_boltz_input }
+
     RUN_BOLTZ(
-        BOLTZ_FASTA.out.formatted_fasta.map{[it[0], it[1]]},
-        BOLTZ_FASTA.out.formatted_fasta.map{it[2]},
+        ch_boltz_input.map{[it[0], it[1]]},
+        ch_boltz_input.map{it[2]},
         ch_boltz_model,
         ch_boltz_ccd
     )