use skip_s4pred flag, removed changelog typos

Author: vagkaratzas

CHANGELOG.md

@@ -9,8 +9,8 @@ Initial release of nf-core/proteinannotator, created with the [nf-core](https://
 
 ### `Added`
 
-- [#60](https://github.com/nf-core/proteinannotator/pull/60) - Added nf-core module `S4PRED_RUNMODEL` for secondary structure prediction (i.e., α-helix, a β-strand or a coil). (by @vagkaratzas). (by @vagkaratzas)
-- [#59](https://github.com/nf-core/proteinannotator/pull/59) - Added nf-core qc and pre-processing subworkflow for amino acid sequences `FAA_SEQFU_SEQKIT`. (by @vagkaratzas). (by @vagkaratzas)
+- [#60](https://github.com/nf-core/proteinannotator/pull/60) - Added nf-core module `S4PRED_RUNMODEL` for secondary structure prediction (i.e., α-helix, a β-strand or a coil). (by @vagkaratzas)
+- [#59](https://github.com/nf-core/proteinannotator/pull/59) - Added nf-core qc and pre-processing subworkflow for amino acid sequences `FAA_SEQFU_SEQKIT`. (by @vagkaratzas)
 - [#57](https://github.com/nf-core/proteinannotator/pull/57) - nf-core tools template update to 3.5.1. (by @vagkaratzas)
 - [#52](https://github.com/nf-core/proteinannotator/pull/52) - Add option to turn off InterProScan for testing
 - [#51](https://github.com/nf-core/proteinannotator/pull/51) - Update to nf-core/tools v3.3.1

main.nf

@@ -39,7 +39,8 @@ workflow NFCORE_PROTEINANNOTATOR {
     //
     PROTEINANNOTATOR (
         samplesheet,
-        params.skip_preprocessing
+        params.skip_preprocessing,
+        params.skip_s4pred
     )
     emit:
     multiqc_report = PROTEINANNOTATOR.out.multiqc_report // channel: /path/to/multiqc_report.html

workflows/proteinannotator.nf

@@ -25,6 +25,7 @@ workflow PROTEINANNOTATOR {
     take:
     ch_samplesheet      // channel: samplesheet read in from --input
     skip_preprocessing  // boolean
+    skip_s4pred         // boolean
 
     main:
 
@@ -45,8 +46,10 @@ workflow PROTEINANNOTATOR {
     FUNCTIONAL_ANNOTATION( ch_samplesheet_updated )
     ch_versions = ch_versions.mix( FUNCTIONAL_ANNOTATION.out.versions.first() )
 
-    S4PRED_RUNMODEL( ch_samplesheet_updated )
-    ch_versions = ch_versions.mix( S4PRED_RUNMODEL.out.versions.first() )
+    if (!skip_s4pred) {
+        S4PRED_RUNMODEL( ch_samplesheet_updated )
+        ch_versions = ch_versions.mix( S4PRED_RUNMODEL.out.versions.first() )
+    }
 
     //
     // Collate and save software versions