Fix Gstring interpolation in getFileExtension

CHANGELOG.md

@@ -61,14 +61,17 @@ Initial release of nf-core/phaseimpute, created with the [nf-core](https://nf-co
 - [#139](https://github.com/nf-core/phaseimpute/pull/139) - Update all nf-core modules
 - [#146](https://github.com/nf-core/phaseimpute/pull/146) - Remove conda CI check for PR due to nextflow error
 - [#144](https://github.com/nf-core/phaseimpute/pull/144) - Documentation updates
+- [#148](https://github.com/nf-core/phaseimpute/pull/148) - Fix awsfulltest github action for manual dispatch
+- [#149](https://github.com/nf-core/phaseimpute/pull/149) - Remove the map file from the awsfulltest
 
 ### `Fixed`
 
 - [#15](https://github.com/nf-core/phaseimpute/pull/15) - Changed test csv files to point to nf-core repository
 - [#16](https://github.com/nf-core/phaseimpute/pull/16) - Removed outdir from test config files
 - [#65](https://github.com/nf-core/phaseimpute/pull/65) - Separate stitch output by individuals
-- [#75](https://github.com/nf-core/phaseimpute/pull/75) - Set frequency computation with VCFFIXUP process as optional with --compute_freq. Use Glimpse_chunk on panel vcf to compute the chunk and not makewindows on fasta.
+- [#75](https://github.com/nf-core/phaseimpute/pull/75) - Set frequency computation with VCFFIXUP process as optional with `--compute_freq`. Use Glimpse_chunk on panel vcf to compute the chunk and not makewindows on fasta.
 - [#117](https://github.com/nf-core/phaseimpute/pull/117) - Fix directories in CSV.
+- [#151](https://github.com/nf-core/phaseimpute/pull/151) - Fix `Type not supported: class org.codehaus.groovy.runtime.GStringImpl` error due to `String` test in `getFileExtension()`.
 
 ### `Dependencies`
 

conf/test_full.config

@@ -29,7 +29,6 @@ params {
     // Input data
     input  = "${projectDir}/tests/csv/sample_sim_full.csv"
     panel  = "${projectDir}/tests/csv/panel_full.csv"
-    map    = "${projectDir}/tests/csv/map.csv"
 
     // Pipeline steps
     steps  = "all"

subworkflows/local/utils_nfcore_phaseimpute_pipeline/main.nf

@@ -502,8 +502,8 @@ def getFileExtension(file) {
             error "Type not supported: ${file} = ${file.getClass()}"
         }
     }
-    if (file instanceof String) {
-        return file.replace(".gz","").split("\\.").last()
+    if (file instanceof CharSequence) {
+        return file.toString().replace(".gz", "").split("\\.").last()
     } else {
         error "Type not supported: ${file.getClass()}"
     }
@@ -617,8 +617,8 @@ def toolCitationText() {
         params.tools ? params.tools.split(',').contains("glimpse2")  ? "GLIMPSE2 (Rubinacci et al. 2023)," : "": "",
         params.tools ? params.tools.split(',').contains("quilt")     ? "QUILT (Davies et al. 2021)," : "": "",
         "SAMtools (Li et al. 2009),",
-        params.tools ? params.phased ? "SHAPEIT5 (Hofmeister et al. 2023)," : "": "",
-        params.tools ? params.phased ? "BEDtools (Quinlan and Hall 2010)," : "": "",
+        params.tools ? params.phase ? "SHAPEIT5 (Hofmeister et al. 2023)," : "": "",
+        params.tools ? params.phase ? "BEDtools (Quinlan and Hall 2010)," : "": "",
         params.tools ? params.tools.split(',').contains("stitch")    ? "STITCH (Davies et al. 2016)," : "": "",
         "Tabix (Li et al. 2011),",
         params.tools ? params.compute_freq  ? "VCFlib (Garrison et al. 2022)," : "": "",
@@ -632,13 +632,13 @@ def toolBibliographyText() {
     // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "<li>Author (2023) Pub name, Journal, DOI</li>" : "",
     // Uncomment function in methodsDescriptionText to render in MultiQC report
     def reference_text = [
-        params.phased ? "<li>Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi:10.1093/bioinformatics/btq033.</li>": "",
+        params.phase ? "<li>Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010 Mar 15;26(6):841-2. doi:10.1093/bioinformatics/btq033.</li>": "",
         "<li>Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi:10.1093/bioinformatics/btp352.</li>",
         "<li>Li H. (2011). Tabix: fast retrieval of sequence features from generic TAB-delimited files. Bioinformatics. 2011 Mar 1;27(5):718-9. doi:10.1093/bioinformatics/btq671.</li>",
         params.tools ? params.tools.split(',').contains("quilt") ? "<li>Davies RW, Kucka M, Su D, Shi S, Flanagan M, Cunniff CM, Chan YF, & Myers S. (2021). Rapid genotype imputation from sequence with reference panels. Nature Genetics. doi:10.1038/s41588-021-00877-0.</li>" : "": "",
         params.tools ? params.tools.split(',').contains("glimpse") ? "<li>Rubinacci S, Ribeiro DM, Hofmeister RJ, & Delaneau O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nature Genetics. doi:10.1038/s41588-020-00756-0.</li>" : "": "",
         params.tools ? params.tools.split(',').contains("glimpse2") ? "<li>Rubinacci S, Hofmeister RJ, Sousa da Mota B, & Delaneau O. (2023). Imputation of low-coverage sequencing data from 150,119 UK Biobank genomes. Nature Genetics. doi:10.1038/s41588-023-01438-3.</li>" : "": "",
-        params.phased ? "<li>Hofmeister RJ, Ribeiro DM, Rubinacci S, Delaneau O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nat Genet. 2023 Jul;55(7):1243-1249. doi:10.1038/s41588-023-01415-w.</li>" : "",
+        params.phase ? "<li>Hofmeister RJ, Ribeiro DM, Rubinacci S, Delaneau O. (2023). Accurate rare variant phasing of whole-genome and whole-exome sequencing data in the UK Biobank. Nat Genet. 2023 Jul;55(7):1243-1249. doi:10.1038/s41588-023-01415-w.</li>" : "",
         params.tools ? params.tools.split(',').contains("stitch") ? "<li>Davies RW, Flint J, Myers S, & Mott R. (2016). Rapid genotype imputation from sequence without reference panels. Nature Genetics.</li>" : "": "",
         params.compute_freq ? "<li>Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS, Prins P. (2022). A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar. PLoS Comput Biol 18(5).</li>" : "",
     ].join(' ').trim()