Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <[email protected]>

Author: jscgh

docs/usage.md

@@ -426,7 +426,7 @@ If you specify the `--esmfold_db <PATH>` parameter, the directory structure of y
     └── esmfold_3B_v1.pt
 ```
 
-HelixFold3 can be run using this command (note that HF3 requires .json files not .fasta):
+HelixFold3 can be run using this command (note that HF3 requires `.json` files not `.fasta`):
 
 ```console
 nextflow run nf-core/proteinfold \

main.nf

@@ -311,10 +311,10 @@ workflow NFCORE_PROTEINFOLD {
             PREPARE_HELIXFOLD3_DBS.out.helixfold3_init_models,
             PREPARE_HELIXFOLD3_DBS.out.helixfold3_maxit_src
         )
-        ch_helixfold3_top_ranked_pdb    = HELIXFOLD3.out.top_ranked_pdb
-        ch_multiqc                      = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
-        ch_versions                     = ch_versions.mix(HELIXFOLD3.out.versions)
-        ch_report_input                 = ch_report_input.mix(HELIXFOLD3.out.pdb_msa)
+        ch_helixfold3_top_ranked_pdb = HELIXFOLD3.out.top_ranked_pdb
+        ch_multiqc                   = ch_multiqc.mix(HELIXFOLD3.out.multiqc_report.collect())
+        ch_versions                  = ch_versions.mix(HELIXFOLD3.out.versions)
+        ch_report_input              = ch_report_input.mix(HELIXFOLD3.out.pdb_msa)
     }
 
     //

modules/local/run_helixfold3/main.nf

@@ -3,7 +3,6 @@
  */
 process RUN_HELIXFOLD3 {
     tag "$meta.id"
-    label 'gpu_compute'
     label 'process_medium'
 
     // Exit if running this module with -profile conda / -profile mamba

subworkflows/local/prepare_helixfold3_dbs.nf

@@ -133,17 +133,17 @@ workflow PREPARE_HELIXFOLD3_DBS {
     }
 
     emit:
-    helixfold3_uniclust30        = ch_helixfold3_uniclust30
-    helixfold3_ccd_preprocessed  = ch_helixfold3_ccd_preprocessed
-    helixfold3_rfam              = ch_helixfold3_rfam
-    helixfold3_bfd               = ch_helixfold3_bfd
-    helixfold3_small_bfd         = ch_helixfold3_small_bfd
-    helixfold3_uniprot           = ch_helixfold3_uniprot
-    helixfold3_pdb_seqres        = ch_helixfold3_pdb_seqres
-    helixfold3_uniref90          = ch_helixfold3_uniref90
-    helixfold3_mgnify            = ch_helixfold3_mgnify
-    helixfold3_pdb_mmcif         = ch_helixfold3_pdb_mmcif
-    helixfold3_init_models       = ch_helixfold3_init_models
-    helixfold3_maxit_src         = ch_helixfold3_maxit_src
-    versions                     = ch_versions
+    helixfold3_uniclust30       = ch_helixfold3_uniclust30
+    helixfold3_ccd_preprocessed = ch_helixfold3_ccd_preprocessed
+    helixfold3_rfam             = ch_helixfold3_rfam
+    helixfold3_bfd              = ch_helixfold3_bfd
+    helixfold3_small_bfd        = ch_helixfold3_small_bfd
+    helixfold3_uniprot          = ch_helixfold3_uniprot
+    helixfold3_pdb_seqres       = ch_helixfold3_pdb_seqres
+    helixfold3_uniref90         = ch_helixfold3_uniref90
+    helixfold3_mgnify           = ch_helixfold3_mgnify
+    helixfold3_pdb_mmcif        = ch_helixfold3_pdb_mmcif
+    helixfold3_init_models      = ch_helixfold3_init_models
+    helixfold3_maxit_src        = ch_helixfold3_maxit_src
+    versions                    = ch_versions
 }

workflows/helixfold3.nf

@@ -7,7 +7,7 @@
 //
 // MODULE: Loaded from modules/local/
 //
-include { RUN_HELIXFOLD3      } from '../modules/local/run_helixfold3'
+include { RUN_HELIXFOLD3 } from '../modules/local/run_helixfold3'
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -40,11 +40,11 @@ workflow HELIXFOLD3 {
     ch_helixfold3_maxit_src
 
     main:
-    ch_multiqc_files    = Channel.empty()
-    ch_pdb              = Channel.empty()
-    ch_top_ranked_pdb   = Channel.empty()
-    ch_msa              = Channel.empty()
-    ch_multiqc_report   = Channel.empty()
+    ch_multiqc_files  = Channel.empty()
+    ch_pdb            = Channel.empty()
+    ch_top_ranked_pdb = Channel.empty()
+    ch_msa            = Channel.empty()
+    ch_multiqc_report = Channel.empty()
 
     //
     // SUBWORKFLOW: Run helixfold3