Now copying files in NCBI_FCS_GX_SETUP_SAMPLE rather than symlinking …

…in an attempt to support NextFlow Fusion
Plant-Food-Research-Open · Jun 3, 2024 · 04fd4a4 · 04fd4a4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -37,6 +37,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 8. Updated `FASTA_LTRRETRIEVER_LAI` to fix a pipeline crash when `ch_monoploid_seqs` was `[ meta, [] ]` [#83](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/83)
 9. Improved input assembly documentation [#86](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/86)
 10. Added assembly tag to synteny warning message regarding missing `synteny_labels` file
+11. Now copying files in `NCBI_FCS_GX_SETUP_SAMPLE` rather than symlinking in an attempt to support NextFlow Fusion
 
 ### `Dependencies`
 

diff --git a/modules/local/ncbi_fcs_gx_setup_sample.nf b/modules/local/ncbi_fcs_gx_setup_sample.nf
@@ -22,7 +22,7 @@ process NCBI_FCS_GX_SETUP_SAMPLE {
         error "NCBI_FCS_GX_SETUP_SAMPLE module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
     """
-    ln -s $fasta_file "fasta.file.for.${asm_tag}.fasta"
+    cp $fasta_file fasta.file.for.${asm_tag}.fasta
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":