From 841ea902528376d36f94ee9d7d9a10b15fbaf9a1 Mon Sep 17 00:00:00 2001
From: Alfred Kedhammar <alfred.kedhammar@scilifelab.se>
Date: Thu, 19 Dec 2024 10:11:53 +0000
Subject: [PATCH] bump module patch

---
 .../fastqscreen/fastqscreen-fastqscreen.diff  | 38 +++++++++----------
 1 file changed, 17 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
index beef4a9..658d149 100644
--- a/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
+++ b/modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff
@@ -1,4 +1,4 @@
-Changes in module 'nf-core/fastqscreen/fastqscreen'
+Changes in component 'nf-core/fastqscreen/fastqscreen'
 Changes in 'fastqscreen/fastqscreen/environment.yml':
 --- modules/nf-core/fastqscreen/fastqscreen/environment.yml
 +++ modules/nf-core/fastqscreen/fastqscreen/environment.yml
@@ -16,7 +16,6 @@ Changes in 'fastqscreen/fastqscreen/environment.yml':
 +  # - bwa
 +  # - bismark
 
-'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
 Changes in 'fastqscreen/fastqscreen/main.nf':
 --- modules/nf-core/fastqscreen/fastqscreen/main.nf
 +++ modules/nf-core/fastqscreen/fastqscreen/main.nf
@@ -37,28 +36,26 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
      output:
      tuple val(meta), path("*.txt")     , emit: txt
-@@ -24,31 +24,45 @@
+@@ -24,31 +24,42 @@
      script:
      def prefix = task.ext.prefix ?: "${meta.id}"
      def args = task.ext.args ?: ""
 +    def config_content = ref_names.withIndex().collect { name, i -> "DATABASE ${name} ./${ref_dirs[i]}/${ref_basenames[i]} ${ref_aligners[i]}" }.join('\n')
-+    def num_reads     = reads instanceof List  ? reads.size() : 1
-+    def mv_txt_cmd    = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.txt ${prefix}_screen.txt" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    def mv_html_cmd   = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.html ${prefix}_1_screen.html" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    def mv_png_cmd    = (num_reads == 1) ? 
-+            "mv ${reads[0].simpleName}_screen.png ${prefix}_1_screen.png" : 
-+            reads.collect { "mv ${it.simpleName}_screen.txt ${prefix}_${it.simpleName}_screen.txt" }.join(' && ')
-+    """
-+    echo '${config_content}' > fastq_screen.conf
  
--    """
++    // Build mv commands to rename the output files. Dual reads will be appended with '_1' and '_2'
++    def num_reads = reads instanceof List  ? reads.size() : 1
++    def file_extensions = ['txt', 'html', 'png']
++    def mv_cmd = file_extensions.collect { ext ->
++        reads.withIndex().collect { read, i ->
++            "mv ${read.simpleName}_screen.${ext} ${prefix}${num_reads > 1 ? "_${i+1}" : ''}_screen.${ext}"
++        }.join(' && ')
++    }.join(' && ')
+     """
 -    fastq_screen --threads ${task.cpus} \\
 -        --aligner bowtie2 \\
 -        --conf ${database}/fastq_screen.conf \\
++    echo '${config_content}' > fastq_screen.conf
++
 +    fastq_screen \\
 +        --conf fastq_screen.conf \\
 +        --threads ${task.cpus} \\
@@ -70,9 +67,7 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
 -    "${task.process}":
 -        fastqscreen: \$(echo \$(fastq_screen --version 2>&1) | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 -    END_VERSIONS
-+    $mv_txt_cmd
-+    $mv_html_cmd
-+    $mv_png_cmd
++    $mv_cmd
 +
 +    fastq_screen_version=\$(fastq_screen --version 2>&1 | sed 's/^.*FastQ Screen v//; s/ .*\$//')
 +    echo "\\\"${task.process}\\\":" > versions.yml
@@ -100,8 +95,9 @@ Changes in 'fastqscreen/fastqscreen/main.nf':
  
  }
 
+'modules/nf-core/fastqscreen/fastqscreen/meta.yml' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test.snap' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
 'modules/nf-core/fastqscreen/fastqscreen/tests/nextflow.config' is unchanged
-'modules/nf-core/fastqscreen/fastqscreen/tests/main.nf.test' is unchanged
+'modules/nf-core/fastqscreen/fastqscreen/tests/tags.yml' is unchanged
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