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Patch wget failure to download #338

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Patch wget failure to download #338

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34380e9
Updated wget sources. Added ftp protocol to fastq url
ukleiner Feb 26, 2025
b249f88
bumped patch version
ukleiner Feb 26, 2025
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10 changes: 5 additions & 5 deletions modules/local/sra_fastq_ftp/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' :
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Is there a reason, why the wget singularity container version is not changed?
The container https://depot.galaxyproject.org/singularity/wget:1.20.1 would be inconsistent with the docker and conda environments or am I missing something?

In issue 328 which you are mentioning people are using singularity. In a quick test changing the container to https://depot.galaxyproject.org/singularity/wget:1.21.4 resolves the issue for me.

'biocontainers/wget:1.20.1' }"
'biocontainers/wget:1.21.4' }"

input:
tuple val(meta), val(fastq)
Expand All @@ -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
Expand All @@ -39,15 +39,15 @@ 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

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
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -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'
}

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