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Fix support for s5cmd 2.2.2 #5069

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merged 1 commit into from
Jun 15, 2024
Merged

Fix support for s5cmd 2.2.2 #5069

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2 changes: 1 addition & 1 deletion plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -162,7 +162,7 @@ class S3BashLib extends BashFunLib<S3BashLib> {
local source=\$1
local target=\$2
local file_name=\$(basename \$1)
local is_dir=\$($cli ls \$source | grep -F "DIR \${file_name}/" -c)
local is_dir=\$($cli ls \$source | grep -F "DIR \${file_name}/" -c)
if [[ \$is_dir == 1 ]]; then
$cli cp "\$source/*" "\$target"
else
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4 changes: 2 additions & 2 deletions plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy
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Expand Up @@ -770,7 +770,7 @@ class S3BashLibTest extends Specification {
local source=$1
local target=$2
local file_name=$(basename $1)
local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
if [[ $is_dir == 1 ]]; then
s5cmd cp "$source/*" "$target"
else
Expand Down Expand Up @@ -807,7 +807,7 @@ class S3BashLibTest extends Specification {
local source=$1
local target=$2
local file_name=$(basename $1)
local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c)
if [[ $is_dir == 1 ]]; then
s5cmd cp "$source/*" "$target"
else
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4 changes: 2 additions & 2 deletions plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
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Expand Up @@ -73,8 +73,8 @@ import org.slf4j.LoggerFactory
@CompileStatic
class WaveClient {

final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json'
final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json'

private static Logger log = LoggerFactory.getLogger(WaveClient)

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10 changes: 5 additions & 5 deletions plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
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Expand Up @@ -1092,11 +1092,11 @@ class WaveClientTest extends Specification {

where:
ARCH | EXPECTED
'linux/amd64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
'linux/x86_64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json'
'arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
'linux/arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
'linux/arm64/v8' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json'
'linux/amd64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json'
'linux/x86_64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json'
'arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json'
'linux/arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json'
'linux/arm64/v8' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json'
}

def 'should configure custom s5cmd' () {
Expand Down