diff --git a/modules/get_fast5_test_data.nf b/modules/get_fast5_test_data.nf index a2b2c0a..f8ca724 100644 --- a/modules/get_fast5_test_data.nf +++ b/modules/get_fast5_test_data.nf @@ -5,7 +5,7 @@ process get_fast5 { path("fast5") script: """ - wget https://osf.io/vxd7f/download -O SARSCoV2.tar.gz + wget --no-check-certificate https://osf.io/vxd7f/download -O SARSCoV2.tar.gz tar xzf SARSCoV2.tar.gz """ } diff --git a/modules/get_fasta_test_data.nf b/modules/get_fasta_test_data.nf index 35bb730..4c8ecac 100644 --- a/modules/get_fasta_test_data.nf +++ b/modules/get_fasta_test_data.nf @@ -5,6 +5,6 @@ process get_fasta { path("SARSCoV2.fasta") script: """ - wget https://osf.io/87bc9/download -O SARSCoV2.fasta + wget --no-check-certificate https://osf.io/87bc9/download -O SARSCoV2.fasta """ } diff --git a/modules/get_fastq_test_data.nf b/modules/get_fastq_test_data.nf index d20ac00..9d89fbb 100644 --- a/modules/get_fastq_test_data.nf +++ b/modules/get_fastq_test_data.nf @@ -4,6 +4,6 @@ process get_nanopore_fastq { path("SARSCoV2.fastq.gz") script: """ - wget https://osf.io/kf54a/download -O SARSCoV2.fastq.gz + wget --no-check-certificate https://osf.io/kf54a/download -O SARSCoV2.fastq.gz """ } diff --git a/workflows/process/download_database_kraken2.nf b/workflows/process/download_database_kraken2.nf index afc8f35..ab6d314 100755 --- a/workflows/process/download_database_kraken2.nf +++ b/workflows/process/download_database_kraken2.nf @@ -6,12 +6,14 @@ process download_database_kraken2 { output: path("kraken.tar.gz") script: - if (task.attempt = 1) + if (task.attempt.toInteger() == 1) """ + echo ${task.attempt} wget --no-check-certificate https://zenodo.org/record/4534746/files/GRCh38.p13_SC2_2021-02-08.tar.gz -O kraken.tar.gz """ - if (task.attempt > 1) + else if (task.attempt.toInteger() > 1) """ + echo ${task.attempt} wget --no-check-certificate https://osf.io/eprfq/download -O kraken.tar.gz """ stub: