From 34380e97a6f16d8632f489675615989e29018c1f Mon Sep 17 00:00:00 2001
From: uri <ukleiner@gmail.com>
Date: Wed, 26 Feb 2025 12:12:21 +0200
Subject: [PATCH 1/2] Updated wget sources. Added ftp protocol to fastq url

---
 modules/local/sra_fastq_ftp/main.nf | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/modules/local/sra_fastq_ftp/main.nf b/modules/local/sra_fastq_ftp/main.nf
index e2274d46..d4ba6038 100644
--- a/modules/local/sra_fastq_ftp/main.nf
+++ b/modules/local/sra_fastq_ftp/main.nf
@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda "conda-forge::wget=1.20.1"
+    conda "conda-forge::wget=1.21.4"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
-        'biocontainers/wget:1.20.1' }"
+        'biocontainers/wget:1.21.4' }"
 
     input:
     tuple val(meta), val(fastq)
@@ -24,7 +24,7 @@ process SRA_FASTQ_FTP {
         wget \\
             $args \\
             -O ${meta.id}.fastq.gz \\
-            ${fastq[0]}
+            ftp://${fastq[0]}
 
         echo "${meta.md5_1}  ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
@@ -39,7 +39,7 @@ process SRA_FASTQ_FTP {
         wget \\
             $args \\
             -O ${meta.id}_1.fastq.gz \\
-            ${fastq[0]}
+            ftp://${fastq[0]}
 
         echo "${meta.md5_1}  ${meta.id}_1.fastq.gz" > ${meta.id}_1.fastq.gz.md5
         md5sum -c ${meta.id}_1.fastq.gz.md5
@@ -47,7 +47,7 @@ process SRA_FASTQ_FTP {
         wget \\
             $args \\
             -O ${meta.id}_2.fastq.gz \\
-            ${fastq[1]}
+            ftp://${fastq[1]}
 
         echo "${meta.md5_2}  ${meta.id}_2.fastq.gz" > ${meta.id}_2.fastq.gz.md5
         md5sum -c ${meta.id}_2.fastq.gz.md5

From b249f8831e8f31a763f3cb3a7f2415254a1022f9 Mon Sep 17 00:00:00 2001
From: uri <ukleiner@gmail.com>
Date: Wed, 26 Feb 2025 12:13:27 +0200
Subject: [PATCH 2/2] bumped patch version

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index bb6b6b79..d4211f27 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -221,7 +221,7 @@ manifest {
     description     = """Pipeline to fetch metadata and raw FastQ files from public databases"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.12.0'
+    version         = '1.12.1'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }