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main.nf

@@ -56,7 +56,7 @@ params.colabfold_alphafold2_params_path = getColabfoldAlphafold2ParamsPath()
 ch_dummy_file = Channel.fromPath("$projectDir/assets/NO_FILE")
 
 workflow NFCORE_PROTEINFOLD {
-    
+
     take:
     samplesheet // channel: samplesheet read in from --input
 
@@ -210,7 +210,7 @@ workflow NFCORE_PROTEINFOLD {
     //
     // TODO: we need to validate the rest of foldseek parameters if foldseek is set to run
     // TODO: maybe create a parameter that is run_foldseek or skip_foldsee instead as there are no more mode than can be use now
-    
+
     // TODO move it to pdb.config? asign as in prepare dbs
     if (params.foldseek_search == "easysearch"){
         ch_foldseek_db = channel.value([
@@ -221,7 +221,7 @@ workflow NFCORE_PROTEINFOLD {
         ])
     }
 
-    ch_multiqc_config        = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first() 
+    ch_multiqc_config        = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true).first()
     ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config ).first()  : Channel.empty()
     ch_multiqc_logo          = params.multiqc_logo   ? Channel.fromPath( params.multiqc_logo ).first()    : Channel.empty()
     ch_multiqc_methods_description = params.multiqc_methods_description ? file(params.multiqc_methods_description, checkIfExists: true) : file("$projectDir/assets/methods_description_template.yml", checkIfExists: true)

modules/local/download_pdbmmcif/main.nf

@@ -10,7 +10,7 @@ process DOWNLOAD_PDBMMCIF {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3c/3c2e1079a0721851248bd2aa45f3d4cd32bfdb7395d609132567d772150965cc/data' :
         'community.wave.seqera.io/library/aria2_rsync:1627a7e9b559cfa0' }"
-    
+
     input:
     val source_url_pdb_mmcif
     val source_url_pdb_obsolete

subworkflows/local/post_processing.nf

@@ -73,13 +73,13 @@ workflow POST_PROCESSING {
 
             COMPARE_STRUCTURES(
                 ch_comparison_report_input
-                    .map { 
-                        it[1][0]["models"] = requested_modes.toLowerCase(); 
+                    .map {
+                        it[1][0]["models"] = requested_modes.toLowerCase();
                         [ it[1][0], it[2] ]
                     },
                 ch_comparison_report_input
                     .map{
-                        it[1][0]["models"] = requested_modes.toLowerCase(); 
+                        it[1][0]["models"] = requested_modes.toLowerCase();
                         [ it[1][0], it[3] ]
                     },
                 ch_comparison_template

workflows/alphafold2.nf

@@ -150,9 +150,9 @@ workflow ALPHAFOLD2 {
 
     ch_pdb
         .join(ch_msa)
-        .map { 
+        .map {
             it[0]["model"] = "alphafold2"
-            it 
+            it
         }
         .set { ch_pdb_msa }
 

workflows/colabfold.nf

@@ -106,14 +106,16 @@ workflow COLABFOLD {
         )
         ch_versions    = ch_versions.mix(COLABFOLD_BATCH.out.versions)
     }
-    
+
     COLABFOLD_BATCH
         .out
         .top_ranked_pdb
         .map { [ it[0]["id"], it[0], it[1] ] }
         .join(
-            COLABFOLD_BATCH.out.msa
-                .map { [ it[0]["id"], it[1] ] }, 
+            COLABFOLD_BATCH
+                .out
+                .msa
+                .map { [ it[0]["id"], it[1] ] },
             remainder:true
         )
         .set { ch_top_ranked_pdb }
@@ -123,8 +125,8 @@ workflow COLABFOLD {
         .pdb
         .join(COLABFOLD_BATCH.out.msa)
         .map {
-            it[0]["model"] = "colabfold" 
-            it 
+            it[0]["model"] = "colabfold"
+            it
         }
         .set { ch_pdb_msa }
 
@@ -135,7 +137,7 @@ workflow COLABFOLD {
         .toSortedList()
         .map { [ [ "model":"colabfold"], it.flatten() ] }
         .set { ch_multiqc_report  }
-    
+
     COLABFOLD_BATCH
         .out
         .multiqc

workflows/esmfold.nf

@@ -62,7 +62,7 @@ workflow ESMFOLD {
         .pdb
         .combine(ch_dummy_file)
         .map {
-            it[0]["model"] = "esmfold" 
+            it[0]["model"] = "esmfold"
             [ it[0]["id"], it[0], it[1], it[2] ]
         }
         .set { ch_top_ranked_pdb }
@@ -84,7 +84,7 @@ workflow ESMFOLD {
             it
         }
         .set { ch_pdb_msa }
-    
+
     ch_pdb_msa
         .map { [ it[0]["id"], it[0], it[1], it[2] ] }
         .set { ch_top_ranked_pdb }