From 89e67fa7534c2654e4a43e81953e1ba611c17df9 Mon Sep 17 00:00:00 2001
From: Edmund Miller <git@edmundmiller.dev>
Date: Tue, 29 Oct 2024 13:00:00 +0100
Subject: [PATCH] fix: Give up on fastq_screen writing it's own config

---
 modules/nf-core/fastqscreen/fastqscreen/main.nf | 12 +++++++-----
 workflows/seqinspector.nf                       |  1 -
 2 files changed, 7 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/main.nf b/modules/nf-core/fastqscreen/fastqscreen/main.nf
index c792707..771c6ac 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/main.nf
+++ b/modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -1,5 +1,5 @@
 process FASTQSCREEN_FASTQSCREEN {
-    tag "$meta.id"
+    tag "$meta.id | $meta2.database_name"
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
@@ -9,7 +9,7 @@ process FASTQSCREEN_FASTQSCREEN {
 
     input:
     tuple val(meta), path(reads)  // .fastq files
-    tuple val(meta), path(database) // [[database_name,  database_notes], database_path]
+    tuple val(meta2), path(database) // [[database_name,  database_notes], database_path]
 
     output:
     tuple val(meta), path("*.txt")     , emit: txt
@@ -26,12 +26,14 @@ process FASTQSCREEN_FASTQSCREEN {
     def args = task.ext.args ?: ""
     // 'Database name','Genome path and basename','Notes'
     """
-    fastq_screen --add_genome \\
-        '$meta.database_name','$database_path','$meta.database_notes'
+    echo "Writing config"
+    echo "DATABASE    ${meta2.database_name}    ./${database}/genome    ${meta2.database_notes}" > fastq_screen.conf
+    echo "Wrote config"
 
-    fastq_screen
+    fastq_screen \\
         --conf fastq_screen.conf \\
         --threads ${task.cpus} \\
+        --aligner ${meta2.database_notes.toLowerCase()} \\
         $reads \\
         $args \\
 
diff --git a/workflows/seqinspector.nf b/workflows/seqinspector.nf
index d283c2a..ad6dc2c 100644
--- a/workflows/seqinspector.nf
+++ b/workflows/seqinspector.nf
@@ -49,7 +49,6 @@ workflow SEQINSPECTOR {
     //
     ch_databases = Channel
         .fromList(samplesheetToList(ch_databasesheet, "${projectDir}/assets/schema_database.json"))
-        .view()
 
     FASTQSCREEN_FASTQSCREEN (
         ch_samplesheet,