use wget instead of curl

CHANGELOG.md

@@ -5,8 +5,30 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Sebastian Uhrig](https://github.com/suhrig)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
+
 ### Enhancements & fixes
 
+- [#169](https://github.com/nf-core/fetchngs/issues/173) - download of big files time out and don't resume
+
+### Software dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `wget`     |             | 1.20.1      |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
 ### Credits

conf/modules.config

@@ -54,7 +54,7 @@ if (params.input_type == 'sra') {
         }
 
         withName: SRA_FASTQ_FTP {
-            ext.args = '--retry 5 --continue-at - --max-time 1200'
+            ext.args = '-t 5 -nv -c -T 60'
             publishDir = [
                 [
                     path: { "${params.outdir}/fastq" },

modules/local/sra_fastq_ftp/main.nf

@@ -4,10 +4,10 @@ process SRA_FASTQ_FTP {
     label 'process_low'
     label 'error_retry'
 
-    conda "bioconda::sra-tools=2.11.0"
+    conda "conda-forge::wget=1.20.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/sra-tools:2.11.0--pl5321ha49a11a_3' :
-        'biocontainers/sra-tools:2.11.0--pl5321ha49a11a_3' }"
+        'https://depot.galaxyproject.org/singularity/wget:1.20.1' :
+        'biocontainers/wget:1.20.1' }"
 
     input:
     tuple val(meta), val(fastq)
@@ -21,40 +21,40 @@ process SRA_FASTQ_FTP {
     def args = task.ext.args ?: ''
     if (meta.single_end) {
         """
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[0]} \\
-            -o ${meta.id}.fastq.gz
+            -O ${meta.id}.fastq.gz \\
+            ${fastq[0]}
 
         echo "${meta.md5_1}  ${meta.id}.fastq.gz" > ${meta.id}.fastq.gz.md5
         md5sum -c ${meta.id}.fastq.gz.md5
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
+            wget: \$(echo \$(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*\$//'))
         END_VERSIONS
         """
     } else {
         """
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[0]} \\
-            -o ${meta.id}_1.fastq.gz
+            -O ${meta.id}_1.fastq.gz \\
+            ${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
 
-        curl \\
+        wget \\
             $args \\
-            -L ${fastq[1]} \\
-            -o ${meta.id}_2.fastq.gz
+            -O ${meta.id}_2.fastq.gz \\
+            ${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
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            curl: \$(echo \$(curl --version | head -n 1 | sed 's/^curl //; s/ .*\$//'))
+            wget: \$(echo \$(wget --version | head -n 1 | sed 's/^GNU Wget //; s/ .*\$//'))
         END_VERSIONS
         """
     }