Merge pull request #241 from nicolae06/dev-Nicolae

Merge fix: "use wget instead of curl #229"

CHANGELOG.md

@@ -3,6 +3,33 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unpublished Version / DEV]
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Alexandru Mizeranschi](https://github.com/nicolae06)
+- [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
+
+- [PR #241](https://github.com/nf-core/fetchngs/pull/241) - Download of big files time out and don't resume ([#169](https://github.com/nf-core/fetchngs/issues/169))
+
+### 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.
+
 ## [[1.11.0](https://github.com/nf-core/fetchngs/releases/tag/1.11.0)] - 2023-10-18
 
 ### Credits
@@ -26,8 +53,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 
 - [PR #188](https://github.com/nf-core/fetchngs/pull/188) - Use nf-test for all pipeline testing
 
-### Enhancements & fixes
-
 ## [[1.10.1](https://github.com/nf-core/fetchngs/releases/tag/1.10.1)] - 2023-10-08
 
 ### Credits

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
         """
     }

modules/local/sra_fastq_ftp/nextflow.config

@@ -1,6 +1,6 @@
 process {
     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/tests/main.nf.test.snap

@@ -11,8 +11,8 @@
                             "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
                         },
                         [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
                         ]
                     ]
                 ],
@@ -31,7 +31,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
                 ],
                 "fastq": [
                     [
@@ -42,8 +42,8 @@
                             "md5_2": "56271be38a80db78ef3bdfc5d9909b98"
                         },
                         [
-                            "SRX9626017_SRR13191702_1.fastq.gz:md5,89c5be920021a035084d8aeb74f32df7",
-                            "SRX9626017_SRR13191702_2.fastq.gz:md5,56271be38a80db78ef3bdfc5d9909b98"
+                            "SRX9626017_SRR13191702_1.fastq.gz:md5,baaaea61cba4294ec696fdfea1610848",
+                            "SRX9626017_SRR13191702_2.fastq.gz:md5,8e43ad99049fabb6526a4b846da01c32"
                         ]
                     ]
                 ],
@@ -62,10 +62,10 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,6b9d69dea1c1305f74a65197ee871f1b"
+                    "versions.yml:md5,6b60ed6d5805271a1b97798e29c0635c"
                 ]
             }
         ],
-        "timestamp": "2023-09-22T10:58:46.998421"
+        "timestamp": "2023-12-20T23:33:35.159073"
     }
 }