From ca0195b1d0e8b39215db83aacbc3f37f5e45832f Mon Sep 17 00:00:00 2001
From: Usman Rashid <usman@smme.edu.pk>
Date: Fri, 19 Jul 2024 08:48:59 +1200
Subject: [PATCH] Updated NCBI FCS GX to 0.5.4

---
 CHANGELOG.md                                |  4 +++-
 modules/local/ncbi_fcs_gx_screen_samples.nf | 20 ++++++++++++++------
 2 files changed, 17 insertions(+), 7 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b8699e30..cfd75cbe 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,7 +14,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 1. Fixed a bug where `intron_length_distribution` was used instead of `cds_length_distribution` when creating the CDS Length Distribution Graph [#95](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/95)
 2. Fixed a bug where 'Subsequent pipeline modules are skipped.' was printed in the `report.html` even when `contamination_stops_pipeline` was set to false
-3. Changed default branch name from `master` to `main` in nf-core template files
+3. Updated NCBI FCS GX to 0.5.4 [#93](https://github.com/Plant-Food-Research-Open/assemblyqc/issues/93)
+4. Now NCBI FCS GX module uses all the cores available from the Nextflow task
+5. Changed default branch name from `master` to `main` in nf-core template files
 
 ### `Dependencies`
 
diff --git a/modules/local/ncbi_fcs_gx_screen_samples.nf b/modules/local/ncbi_fcs_gx_screen_samples.nf
index f9ed5cc8..24276f61 100644
--- a/modules/local/ncbi_fcs_gx_screen_samples.nf
+++ b/modules/local/ncbi_fcs_gx_screen_samples.nf
@@ -2,10 +2,10 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     tag 'all samples'
     label 'process_high'
 
-    conda "bioconda::ncbi-fcs-gx=0.5.0"
+    conda "bioconda::ncbi-fcs-gx=0.5.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.0--h4ac6f70_3':
-        'biocontainers/ncbi-fcs-gx:0.5.0--h4ac6f70_3' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-fcs-gx:0.5.4--h4ac6f70_0':
+        'biocontainers/ncbi-fcs-gx:0.5.4--h4ac6f70_0' }"
 
     input:
     path samples
@@ -21,12 +21,20 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     task.ext.when == null || task.ext.when
 
     script:
-    def VERSION = 0.5
+    def VERSION = '0.5.4'
     """
+    export GX_NUM_CORES=$task.cpus
+
     for sample_fasta in $samples;
     do
         sample_tag=\$(echo "\$sample_fasta" | sed 's/fasta.file.for.//g' | sed 's/.fasta//g')
-        run_gx.py --fasta ./\$sample_fasta --out-dir ./ --gx-db $db_path --tax-id "${tax_id}"
+
+        run_gx.py \\
+            --fasta ./\$sample_fasta \\
+            --out-dir ./ \\
+            --gx-db $db_path \\
+            --tax-id "${tax_id}" \\
+            --phone-home-label github/$workflow.manifest.name
 
         mv "\${sample_fasta%.fasta}.${tax_id}.fcs_gx_report.txt" "\${sample_tag}.fcs_gx_report.txt"
         mv "\${sample_fasta%.fasta}.${tax_id}.taxonomy.rpt" "\${sample_tag}.taxonomy.rpt"
@@ -39,7 +47,7 @@ process NCBI_FCS_GX_SCREEN_SAMPLES {
     """
 
     stub:
-    def VERSION = 0.5
+    def VERSION = '0.5.4'
     """
     for sample_fasta in $samples;
     do