Merge pull request #297 from nf-core/start-qc

Add QC check for empty files out of annotation
nf-core · Jul 20, 2023 · 2a5c3ee · 2a5c3ee
2 parents 3bce3b4 + 9d16c0d
commit 2a5c3ee
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Showing 2 changed files with 40 additions and 4 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,12 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#290](https://github.com/nf-core/funcscan/pull/290) Merged pipeline template of nf-core/tools version 2.9, updated references. (by @jfy133)
 - [#285](https://github.com/nf-core/funcscan/pull/285) Use nf-validation for samplesheet checking and added support for `fna.gz` input FASTA files (by @louperelo, @mirpedrol, @jfy133)
-
 - [#295](https://github.com/nf-core/funcscan/pull/295) Add Prokka to MultiQC output (by @louperelo)
 
 ### `Fixed`
 
 - [#296](https://github.com/nf-core/funcscan/pull/296) Fixed empty output when saving prodigal annotations. (reported by @louperelo, fix by @jasmezz)
+- [#297](https://github.com/nf-core/funcscan/pull/297) Added check for empty annotation files prior going into screening. (❤️ to @alexhbnr for requesting, added by @jfy133)
 
 ### `Dependencies`
 

diff --git a/workflows/funcscan.nf b/workflows/funcscan.nf
@@ -243,7 +243,15 @@ workflow FUNCSCAN {
         AMPs
     */
     if ( params.run_amp_screening ) {
-        AMP ( ch_prepped_input, ch_annotation_faa )
+        AMP (
+            ch_prepped_input,
+            ch_annotation_faa
+                .filter {
+                    meta, file ->
+                        if ( file.isEmpty() ) log.warn("Annotation of following sample produced produced an empty FAA file. AMP screening tools requiring this file will not be executed: ${meta.id}")
+                        !file.isEmpty()
+                }
+        )
         ch_versions = ch_versions.mix(AMP.out.versions)
     }
 
@@ -254,7 +262,15 @@ workflow FUNCSCAN {
         if (params.arg_skip_deeparg) {
             ARG ( ch_prepped_input, [] )
         } else {
-            ARG ( ch_prepped_input, ch_annotation_faa )
+            ARG (
+                ch_prepped_input,
+                ch_annotation_faa
+                    .filter {
+                        meta, file ->
+                        if ( file.isEmpty() ) log.warn("Annotation of following sample produced produced an empty FAA file. AMP screening tools requiring this file will not be executed: ${meta.id}")
+                            !file.isEmpty()
+                    }
+            )
         }
         ch_versions = ch_versions.mix(ARG.out.versions)
     }
@@ -263,7 +279,27 @@ workflow FUNCSCAN {
         BGCs
     */
     if ( params.run_bgc_screening ) {
-        BGC ( ch_prepped_input, ch_annotation_gff, ch_annotation_faa, ch_annotation_gbk )
+        BGC (
+            ch_prepped_input,
+            ch_annotation_gff
+                .filter {
+                    meta, file ->
+                        if ( file.isEmpty() ) log.warn("Annotation of following sample produced produced an empty GFF file. AMP screening tools requiring this file will not be executed: ${meta.id}")
+                        !file.isEmpty()
+                },
+            ch_annotation_faa
+                .filter {
+                    meta, file ->
+                        if ( file.isEmpty() ) log.warn("Annotation of following sample produced produced an empty FAA file. AMP screening tools requiring this file will not be executed: ${meta.id}")
+                        !file.isEmpty()
+                },
+            ch_annotation_gbk
+                .filter {
+                    meta, file ->
+                        if ( file.isEmpty() ) log.warn("Annotation of following sample produced produced an empty GBK file. AMP screening tools requiring this file will not be executed: ${meta.id}")
+                        !file.isEmpty()
+                }
+        )
         ch_versions = ch_versions.mix(BGC.out.versions)
     }