diff --git a/docs/usage.md b/docs/usage.md index a10b93c..9e02fde 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -542,3 +542,37 @@ then { assert snapshot(sanitizeOutput(process.out, unstableKeys:["zip"])).match() } ``` + +### `curlAndExtract()` - Download and extract an archive + +The `curlAndExtract()` function is used to download an archive +from the Internet with `curl` and extract it in the required destination +directory. +Zip and Tar archives are currently supported. Tar archives can be compressed +with any of these algorithms: gzip, gz, bzip2, bz2, xz, lz4, lzma, lzop, zstd. +By default, the choice of archive format and compression algorithm is based on +the name of the archive, but it can also be passed as an argument. +For compressed Tar archives, the format to provide is "tar.bz2" or "tbz2" +(adapting to your compression algorithm of choice). + +You are responsible for deleting the data in the `cleanup` phase. + +```groovy +setup { + curlAndExtract("https://www.example.com/pretty_database.zip", "${launchDir}/data_dir") + curlAndExtract("https://www.example.com/beautiful_database.tar.gz", "${launchDir}/data_dir") + curlAndExtract("https://www.example.com/secret/data", "${launchDir}/data_dir", "tar.bz2") +} + +when { + params { + pretty_db_path = "${launchDir}/data_dir/pretty_db" + beautiful_db_path = "${launchDir}/data_dir/db/beauty_db" + secret_db_path = "${launchDir}/data_dir/db/secret" + } +} + +cleanup { + new File("${launchDir}/data_dir").deleteDir() +} +``` diff --git a/src/main/java/nf_core/nf/test/utils/Methods.java b/src/main/java/nf_core/nf/test/utils/Methods.java index 646985f..9696fd2 100644 --- a/src/main/java/nf_core/nf/test/utils/Methods.java +++ b/src/main/java/nf_core/nf/test/utils/Methods.java @@ -3,11 +3,8 @@ import java.io.BufferedReader; import java.io.File; import java.io.FileReader; -import java.io.FileWriter; import java.io.IOException; -import java.io.InputStreamReader; import java.io.UnsupportedEncodingException; -import java.nio.file.FileAlreadyExistsException; import java.nio.file.FileSystems; import java.nio.file.FileVisitResult; import java.nio.file.Files; @@ -19,12 +16,6 @@ import java.security.MessageDigest; import java.security.NoSuchAlgorithmException; import java.util.*; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Collections; -import java.util.HashMap; -import java.util.List; -import java.util.Map; import java.util.stream.Collectors; import org.yaml.snakeyaml.Yaml; @@ -752,4 +743,203 @@ public static TreeMap sanitizeOutput(TreeMap chann public static TreeMap sanitizeOutput(HashMap options, TreeMap channel) { return OutputSanitizer.sanitizeOutput(options, channel); } + + /** + * Download a tar archive and extract it in the given destination directory. + * The file is streamed directly with `curl` into `tar` via a pipe. + * The compression type must be provided if applicable. + * Uses safe single-quoting for the URL and destination path. + * + * @param urlString the URL to fetch + * @param destPath directory to extract the tarball into + * @param compression compression type: tar, gzip, gz, bzip2, bz2, xz, lz4, lzma, lzop, zstd + * or any of these prefixed with "tar." or "t" + * @throws IOException on failure + */ + private static void curlAndUntar(String urlString, String destPath, String compression) throws IOException { + Path destDir = Paths.get(destPath); + Files.createDirectories(destDir); + + String escUrl = Utils.shellEscape(urlString); + String escDest = Utils.shellEscape(destPath); + String cmd = "curl -L --retry 5 " + escUrl + " | tar xaf - -C " + escDest; + + // Convert compression name to tar option + if (compression != null && !compression.equals("tar")) { + // Remove leading "tar." or "t" if present + if (compression.startsWith("tar.")) { + compression = compression.substring(4); + } else if (compression.startsWith("t")) { + compression = compression.substring(1); + } + + if (compression.equals("gzip") || compression.equals("gz")) { + compression = "gzip"; + } else if (compression.equals("bzip2") || compression.equals("bz2")) { + compression = "bzip2"; + } else if (compression.equals("xz")) { + compression = "xz"; + } else if (compression.equals("lz4")) { + compression = "lz4"; + } else if (compression.equals("lzma")) { + compression = "lzma"; + } else if (compression.equals("lzop")) { + compression = "lzop"; + } else if (compression.equals("zstd") || compression.equals("zst")) { + compression = "zstd"; + } else { + throw new IllegalArgumentException("Unsupported compression type: " + compression); + } + cmd += " --" + compression; + } + + ProcessBuilder pb = new ProcessBuilder("sh", "-c", cmd); + try { + Utils.ProcessResult result = Utils.runProcess(pb); + if (result.exitCode != 0) { + System.err.println("Error downloading and extracting file " + urlString + ": exit code " + result.exitCode + "\n"); + System.out.println("Bash command: \n" + cmd); + System.err.println("command output: \n"); + System.err.println(result.stderr); + } else { + System.out.println("Successfully downloaded and extracted file: " + urlString); + } + } catch (IOException | InterruptedException e) { + System.err.println("Error downloading and extracting file " + urlString + ": " + e.getMessage()); + if (e instanceof InterruptedException) { + Thread.currentThread().interrupt(); + } + } + } + + /** + * Download a zip file and extract it in the given destination directory. + * The file is first downloaded with `curl` to a temporary file, then we + * call `unzip` and delete the temporary file. + * + * @param urlString the URL to fetch + * @param destPath directory to extract the zip into + * @throws IOException on failure + */ + private static void curlAndUnzip(String urlString, String destPath) throws IOException { + Path destDir = Paths.get(destPath); + Files.createDirectories(destDir); + + // Create a temporary file in the destination directory for the downloaded zip + Path tempFile = Files.createTempFile(destDir, "download", ".zip"); + + // Run curl + ProcessBuilder pb = new ProcessBuilder( + "curl", + "-L", + "--retry", + "5", + "-o", + tempFile.toString(), + urlString + ); + + try { + Utils.ProcessResult result = Utils.runProcess(pb); + if (result.exitCode != 0) { + System.err.println("Error downloading file " + urlString + ": exit code " + result.exitCode + "\n"); + System.out.println("Command: " + String.join(" ", pb.command())); + System.err.println("command output: \n"); + System.err.println(result.stderr); + return; + } + // Run unzip + pb = new ProcessBuilder( + "unzip", + "-o", + tempFile.toString(), + "-d", + destPath + ); + result = Utils.runProcess(pb); + if (result.exitCode != 0) { + System.err.println("Error extracting zip " + tempFile + ": exit code " + result.exitCode + "\n"); + System.out.println("Command: " + String.join(" ", pb.command())); + System.err.println("command output: \n"); + System.err.println(result.stderr); + } else { + System.out.println("Successfully downloaded and extracted file: " + urlString); + } + } catch (IOException | InterruptedException e) { + System.err.println("Error downloading and extracting file " + urlString + ": " + e.getMessage()); + if (e instanceof InterruptedException) { + Thread.currentThread().interrupt(); + } + } finally { + try { + Files.deleteIfExists(tempFile); + } catch (IOException e) { + // Do not fail the operation if temp file cleanup fails; just log it + System.err.println("Warning: failed to delete temporary file " + tempFile + ": " + e.getMessage()); + } + } + } + + /** + * Download an archive and extract it in the given destination directory. + * Dispatches to `curlAndUnzip` for ZIP files and to `curlAndUntar` for + * tar archives based on the URL's file extension. + * + * @param urlString the URL to fetch + * @param destPath directory to extract the archive into + * @throws IOException on failure or if archive type is unsupported + */ + public static void curlAndExtract(String urlString, String destPath) throws IOException { + String lower = Utils.getURLFileName(urlString); + + if (lower.endsWith(".zip")) { + curlAndUnzip(urlString, destPath); + return; + } + + for (String suffix: new String [] {"gz", "bz2", "xz", "lz4", "lzma", "lzop", "zst", "zstd"}) { + if (lower.endsWith(".tar." + suffix) || lower.endsWith(".t" + suffix)) { + curlAndUntar(urlString, destPath, suffix); + return; + } + } + + if (lower.endsWith(".tar")) { + curlAndUntar(urlString, destPath, null); + return; + } + + throw new IllegalArgumentException("Unsupported archive type in URL: " + urlString); + } + + /** + * Download an archive and extract it in the given destination directory. + * Dispatches to `curlAndUnzip` for ZIP files and to `curlAndUntar` for + * tar archives based on the `compression` parameter. + * + * @param urlString the URL to fetch + * @param destPath directory to extract the archive into + * @param compression compression type: zip, tar, or any of the following prefixed with "tar." or "t": + * gzip, gz, bzip2, bz2, xz, lz4, lzma, lzop, zstd + * @throws IOException on failure or if archive type is unsupported + */ + public static void curlAndExtract(String urlString, String destPath, String compression) throws IOException { + if (compression == null || compression.isEmpty()) { + throw new IllegalArgumentException("The 'compression' parameter is required."); + } + String lower = compression.toLowerCase(Locale.ROOT); + // Zip is the only clearly defined archive format. + // Everything else is assumed to be Tar + if (lower.equals("zip")) { + curlAndUnzip(urlString, destPath); + } else if (lower.equals("tar")) { + curlAndUntar(urlString, destPath, null); + } else if (lower.startsWith("tar.")) { + curlAndUntar(urlString, destPath, compression); + } else if (lower.startsWith("t")) { + curlAndUntar(urlString, destPath, compression); + } else { + throw new IllegalArgumentException("Unsupported compression type: " + compression); + } + } } diff --git a/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java b/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java index 98ccd55..81ade27 100644 --- a/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java +++ b/src/main/java/nf_core/nf/test/utils/NfCoreUtils.java @@ -1,10 +1,8 @@ package nf_core.nf.test.utils; -import java.io.BufferedReader; import java.io.File; import java.io.FileWriter; import java.io.IOException; -import java.io.InputStreamReader; import java.nio.file.Files; import java.util.LinkedHashMap; import java.util.List; @@ -99,23 +97,14 @@ private static void installModule(String libDir, String name, String sha, String } ProcessBuilder processBuilder = new ProcessBuilder("bash", "-c", command.toString()); - Process process = processBuilder.start(); - - // Capture stderr from nf-core tools - BufferedReader stderrReader = new BufferedReader(new InputStreamReader(process.getErrorStream())); - StringBuilder stderr = new StringBuilder(); - String line; - while ((line = stderrReader.readLine()) != null) { - stderr.append(line).append("\n"); - } - int exitCode = process.waitFor(); + Utils.ProcessResult result = Utils.runProcess(processBuilder); // Spit out nf-core tools stderr if install fails - if (exitCode != 0) { - System.err.println("Error installing module " + name + ": exit code " + exitCode + "\n"); + if (result.exitCode != 0) { + System.err.println("Error installing module " + name + ": exit code " + result.exitCode + "\n"); System.out.println("Installation command: \n" + command.toString()); System.err.println("nf-core tools output: \n"); - System.err.println(stderr.toString()); + System.err.println(result.stderr); } else { System.out.println("Successfully installed module: " + name); } diff --git a/src/main/java/nf_core/nf/test/utils/Utils.java b/src/main/java/nf_core/nf/test/utils/Utils.java new file mode 100644 index 0000000..109241e --- /dev/null +++ b/src/main/java/nf_core/nf/test/utils/Utils.java @@ -0,0 +1,69 @@ +package nf_core.nf.test.utils; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.util.Locale; + +public class Utils { + + /** + * Result of running a process started from a {@link ProcessBuilder}. + */ + public static class ProcessResult { + public final int exitCode; + public final String stderr; + + public ProcessResult(int exitCode, String stderr) { + this.exitCode = exitCode; + this.stderr = stderr; + } + } + + /** + * Starts the given {@link ProcessBuilder}, captures stderr, waits for exit, + * and returns a {@link ProcessResult}. + */ + public static ProcessResult runProcess(ProcessBuilder pb) throws IOException, InterruptedException { + pb.redirectOutput(ProcessBuilder.Redirect.DISCARD); + Process process = pb.start(); + BufferedReader stderrReader = new BufferedReader(new InputStreamReader(process.getErrorStream())); + StringBuilder stderr = new StringBuilder(); + String line; + while ((line = stderrReader.readLine()) != null) { + stderr.append(line).append("\n"); + } + int exitCode = process.waitFor(); + return new ProcessResult(exitCode, stderr.toString()); + } + + /** + * Shell escape a string by wrapping in single quotes and escaping existing single quotes. + * @param s + * @return The shell-escaped string + */ + public static String shellEscape(String s) { + if (s == null) return "''"; + return "'" + s.replace("'", "'" + "\"'\"" + "'") + "'"; + } + + /** + * Extract a lower-cased file name portion from a URL string for extension checking. + * @param urlString The URL string + * @return The lower-cased file name portion of the URL + */ + public static String getURLFileName(String urlString) { + // Try to extract a path portion from the URL (strip query strings) + String pathPart = urlString; + try { + java.net.URI uri = new java.net.URI(urlString); + if (uri.getPath() != null && !uri.getPath().isEmpty()) { + pathPart = uri.getPath(); + } + } catch (Exception e) { + // If parsing fails, fall back to raw urlString + pathPart = urlString; + } + return pathPart.toLowerCase(Locale.ROOT); + } +} diff --git a/tests/curlAndExtract/main.nf b/tests/curlAndExtract/main.nf new file mode 100644 index 0000000..120927c --- /dev/null +++ b/tests/curlAndExtract/main.nf @@ -0,0 +1,9 @@ +process TEST_MODULE { + output: + path ("test.txt"), emit: output + + script: + """ + echo "hello!" > test.txt + """ +} diff --git a/tests/curlAndExtract/main.nf.test b/tests/curlAndExtract/main.nf.test new file mode 100644 index 0000000..bcf96d6 --- /dev/null +++ b/tests/curlAndExtract/main.nf.test @@ -0,0 +1,106 @@ +nextflow_process { + + name "Test Process curlAndExtract" + script "./main.nf" + process "TEST_MODULE" + + tag "test" + + test("test curlAndExtract - tar file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/index/igblast/igblast_base.tar", "${launchDir}/dbs") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract - tar.gz file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/generic/tar/hello.tar.gz", "${launchDir}/dbs") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract - zip file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip", "${launchDir}/dbs") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract with type - tar file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/genome/index/igblast/igblast_base.tar", "${launchDir}/dbs", "tar") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract with type - tar.gzip file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/generic/tar/hello.tar.gz", "${launchDir}/dbs", "tar.gzip") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract with type - zip file") { + + setup { + curlAndExtract("https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/sarscov2/genome/db/maltextract/ncbi_taxmap.zip", "${launchDir}/dbs", "zip") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } + + test("test curlAndExtract with type - tbzip2 file") { + + setup { + curlAndExtract("https://card.mcmaster.ca/latest/data", "${launchDir}/dbs", "tbzip2") + } + then { + def files = getAllFilesFromDir("${launchDir}/dbs") + assert snapshot(files).match() + } + cleanup { + new File("${launchDir}/dbs").deleteDir() + } + } +} diff --git a/tests/curlAndExtract/main.nf.test.snap b/tests/curlAndExtract/main.nf.test.snap new file mode 100644 index 0000000..ac9beb6 --- /dev/null +++ b/tests/curlAndExtract/main.nf.test.snap @@ -0,0 +1,891 @@ +{ + "test curlAndExtract with type - tar file": { + "content": [ + [ + "airr_c_human.tar:md5,a29a0c8d1520ff884e873d9a114684f6", + "airr_c_mouse.tar:md5,b46a8b195eb6d15ed3f84fc51434d126", + "imgt_aa_human_ig_v.pdb:md5,bca60bc424936bd3049579b9d904106b", + "imgt_aa_human_ig_v.phr:md5,95b6ccbf8b5035e4ed224516c3d0ef91", + "imgt_aa_human_ig_v.pin:md5,beb81f86dfd78b84d100049adadd8736", + "imgt_aa_human_ig_v.pjs:md5,8b6a254db719992d738febc70fbfc340", + "imgt_aa_human_ig_v.pog:md5,cc647a49e1a8f3054d9dc28d8ad963fe", + "imgt_aa_human_ig_v.pos:md5,83f0e145736976dcb2588d547b468b84", + "imgt_aa_human_ig_v.pot:md5,6e4f2ab5fce4ab1ce32894e6e0461547", + "imgt_aa_human_ig_v.psq:md5,1050c1905867e66eb6d6ed82ca81966f", + "imgt_aa_human_ig_v.ptf:md5,de1250813f0c7affc6d12dac9d0fb6bb", + "imgt_aa_human_ig_v.pto:md5,192d4564c68d5e02b06978fc001ac933", + "imgt_aa_human_tr_v.pdb:md5,b20fb1d634bcac4e7b3b641f46ee6572", + "imgt_aa_human_tr_v.phr:md5,db542a16a852056e01fc373c481d82ec", + "imgt_aa_human_tr_v.pin:md5,b1029173840eb6a118c103feac3f7e7a", + "imgt_aa_human_tr_v.pjs:md5,e352b4ffa68c204068c3c0398f1c8f06", + "imgt_aa_human_tr_v.pog:md5,aab4b8fdc68806d86dd8a66c21c9721d", + "imgt_aa_human_tr_v.pos:md5,abf41ed496f63ef73be355bfe9315d33", + "imgt_aa_human_tr_v.pot:md5,4bda50a4bf1154c98fcc644da73863bf", + "imgt_aa_human_tr_v.psq:md5,02a78615a1d0630d98a323be4bc34fc1", + "imgt_aa_human_tr_v.ptf:md5,de1250813f0c7affc6d12dac9d0fb6bb", + "imgt_aa_human_tr_v.pto:md5,4af9dffb2f255cb43b31c994f2aec269", + "imgt_aa_mouse_ig_v.pdb:md5,58ea125f6ab44075e31bd89324263398", + "imgt_aa_mouse_ig_v.phr:md5,248cbba3aadbdf814da8706f666c9f91", + "imgt_aa_mouse_ig_v.pin:md5,d6e3e85522830f9c07a3ca23638b1645", + "imgt_aa_mouse_ig_v.pjs:md5,3676804d02cab0a65c0d62b5ab3eb350", + "imgt_aa_mouse_ig_v.pog:md5,6fe25de2b124ecf14453d8507ab536fa", + "imgt_aa_mouse_ig_v.pos:md5,bd4f375790dd4c2ac0fb9627387d6112", + "imgt_aa_mouse_ig_v.pot:md5,81c46146154842750edbc3923e291198", + "imgt_aa_mouse_ig_v.psq:md5,5ec21c57d53c2313513076565b8fbe32", + "imgt_aa_mouse_ig_v.ptf:md5,de1250813f0c7affc6d12dac9d0fb6bb", + "imgt_aa_mouse_ig_v.pto:md5,688627d85d01244e960293af8801aa6b", + "imgt_aa_mouse_tr_v.pdb:md5,fdebe60bd497eed071bed4bf9e2c2c23", + "imgt_aa_mouse_tr_v.phr:md5,ce80dacb605c6fc3f4af0cbd1eff9f8d", + "imgt_aa_mouse_tr_v.pin:md5,7b205e758c0d20885e60d43d4ed951f5", + "imgt_aa_mouse_tr_v.pjs:md5,b2c080a95c7cb06442409b42de0b260e", + "imgt_aa_mouse_tr_v.pog:md5,6c016394ec2c70ae8c89827f49b977a7", + "imgt_aa_mouse_tr_v.pos:md5,b735b8fe72a2e279ae8cc603fe6e973b", + "imgt_aa_mouse_tr_v.pot:md5,4ce6eda1c5ae1f7dea5540256c0349b9", + "imgt_aa_mouse_tr_v.psq:md5,b8c61da709681a273f414d7013a0870b", + 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+ "imgt_aa_mouse_ig_v.fasta:md5,edac8c37e0408f9f6c8d232d79ffc8be", + "imgt_aa_mouse_tr_v.fasta:md5,3e172585de3b78916c2711c5f3ddcb25", + "imgt_human_ig_c.fasta:md5,d660c41cc2bec165cd5ace32405eff39", + "imgt_human_ig_d.fasta:md5,935b4bb5442897f8d97051a4f2fe37d0", + "imgt_human_ig_j.fasta:md5,d7c28fd1c42b3d72b630e290d76fe409", + "imgt_human_ig_v.fasta:md5,0f604ba84709db16f9d4f0eafbd261ba", + "imgt_human_tr_c.fasta:md5,71b3865449c1a42a9e4f59b3ecdf3256", + "imgt_human_tr_d.fasta:md5,fe5ac92ba4d4e2ef0a001685e07b3914", + "imgt_human_tr_j.fasta:md5,dcae2f9293af89398f5df0b4acd60981", + "imgt_human_tr_v.fasta:md5,bcb1b21e6943da537f1e7fdcfce31119", + "imgt_mouse_ig_c.fasta:md5,b778e2bcea4e0a170404b28bd648522c", + "imgt_mouse_ig_d.fasta:md5,aa246ba4e5fa2eaad83ac7daab234772", + "imgt_mouse_ig_j.fasta:md5,3b220b309cc4d15b4cb120aae9e88170", + "imgt_mouse_ig_v.fasta:md5,875b17ff8b5ab819c3e1b332492c494d", + "imgt_mouse_tr_c.fasta:md5,b476e7d4fbd8768ace3877633c6b22de", + "imgt_mouse_tr_d.fasta:md5,3cf6735d31ca794bcf684fa2ccc3d148", + "imgt_mouse_tr_j.fasta:md5,4ef4d35a0e1d770873ae84dd0336d475", + "imgt_mouse_tr_v.fasta:md5,db73f796a88b77f1bbf2964f57a02285", + "human.ndm.imgt:md5,d6cea490480cecfeb082c66607126ff0", + "human.ndm.kabat:md5,294da2ace8c28701ba26406226acf9af", + "human.pdm.imgt:md5,eee1e720fe17bc2b74055dad690c5c3c", + "human.pdm.kabat:md5,2a09fe4aafb06a24ae09866ee2e874e2", + "human_TR_V.nhr:md5,05e85d4422ddd63b251798ad52afbb07", + "human_TR_V.nin:md5,479cf56d41b7708db836278c6090297a", + "human_TR_V.nog:md5,27b8711de1d9cb4a09de4fffd52cd7b4", + "human_TR_V.nsd:md5,1bd3fc688986ca1cd3cbf0ba341e6e88", + "human_TR_V.nsi:md5,902ee2023646ab9d5c2e8bd9e7cd9a74", + "human_TR_V.nsq:md5,1d6eaff8a9696dfb81f54c253adb3e8f", + "human_TR_V.phr:md5,289fad3fda3ca9a4b9dc62a436bb8ba1", + "human_TR_V.pin:md5,b974c4c2e06a7b15e8113b8a114e2a01", + "human_TR_V.pog:md5,0e477541fc88a535d10ec37531198245", + "human_TR_V.psd:md5,9afcedfab46fdad1283dc6932796a56f", + "human_TR_V.psi:md5,9247ca05fe82fb5a528120b3098108b3", + "human_TR_V.psq:md5,4a127b625dcef63b5d0412f7b3e7972b", + "human_V.nhr:md5,18e1447dbb688d21f30781c0a3602cb2", + "human_V.nin:md5,34d4976f789560a3f954203bb8765e2e", + "human_V.nog:md5,3308e60e960e48c12c4a0446aa2ce485", + "human_V.nsd:md5,34506dc9f4d6d385942ea574806669e3", + "human_V.nsi:md5,387635abc8f8ca09293b0bf792bbbfb8", + "human_V.nsq:md5,d3ebdd064a158bdde2708cd19c9cd7d9", + "human_V.phr:md5,d461e9be5047f30963ee7b78c963553a", + "human_V.pin:md5,c0f35ffe97886fe2025a15a829c48749", + "human_V.pog:md5,2aaff4653db578472761e0759b64a768", + "human_V.psd:md5,d1f08d3c624a3770b1232addd7668508", + "human_V.psi:md5,887ac2a9d4cc0e69a94b7543629ab784", + "human_V.psq:md5,35791ac164354b70ad4a35ad9f486f2f", + "mouse.ndm.imgt:md5,352c7f46597497ebf713698fa440ed95", + "mouse.ndm.kabat:md5,2720ae1c09623777e37a116cf9f73823", + "mouse.pdm.imgt:md5,e97ea4cec66d10bceee1ce3518c44082", + "mouse.pdm.kabat:md5,fbce28354f68f4cb6be6333eff6aa0dc", + "mouse_TR_V.nhr:md5,d116d1ef618402cfdbfa75f267813608", + "mouse_TR_V.nin:md5,fcec1baff7bcbe28e71a1e00c24efab7", + "mouse_TR_V.nog:md5,e3dda143f2afc7aa44eb22524049d98e", + "mouse_TR_V.nsd:md5,2d642f4bb76f77bd38f8737f58e9f0f0", + "mouse_TR_V.nsi:md5,9aa022b79d9d063f61ea591ff7a88e7d", + "mouse_TR_V.nsq:md5,61a73abedabb5e8963671f725beb2873", + "mouse_TR_V.phr:md5,4e7cfac13eb50b0b8d8e6d3d49bc5b76", + "mouse_TR_V.pin:md5,2d66648ed028872ac56338a666237a02", + "mouse_TR_V.pog:md5,54a77b456076c55bab9262c76fd7f54f", + "mouse_TR_V.psd:md5,b91ac864d59b2bf1f271255e86c17294", + "mouse_TR_V.psi:md5,b9df1a625a63b5d74499b8c8d7d02e9a", + "mouse_TR_V.psq:md5,6d996ab0e41026b1e28438f25d43c359", + "mouse_V.nhr:md5,32e46aa6a9b13c2e6058a57b11a1cb38", + "mouse_V.nin:md5,319645b00f94d159208f8204c192e89c", + "mouse_V.nog:md5,2c59132ed7f37b70751aeb4264409942", + "mouse_V.nsd:md5,33b7ada29dd6f6b1d848cecffcbfca25", + "mouse_V.nsi:md5,301886dfff9ed7550ab3a2d0b3d916eb", + "mouse_V.nsq:md5,8235994044728f17e8e685d42a01ffae", + "mouse_V.phr:md5,300cf56525199abafa7f69d21ec90d7f", + "mouse_V.pin:md5,32f2c58b40925b798b8c07c98520c625", + "mouse_V.pog:md5,cab625c3365b65a1bf041cf7dbae15b1", + "mouse_V.psd:md5,e981f48453020d8555feec4c6e40cd70", + "mouse_V.psi:md5,d0cd444dc6de67a8e240be0fef5d5949", + "mouse_V.psq:md5,971b28104884d594b328a249e06f7ee1", + "rabbit.ndm.imgt:md5,29910940f8994455d5b632effdb4571f", + "rabbit.ndm.kabat:md5,2a45cb3a7c9e5d103ad6ef1cba3253a9", + "rabbit.pdm.imgt:md5,3ad8b9bb42c7c1e17929cf89f32c549b", + "rabbit.pdm.kabat:md5,5943bba3fcd0d1ba7234843e65876f1f", + "rabbit_V.nhr:md5,83bce87d624c8bd7be460050b81c624d", + "rabbit_V.nin:md5,4b831ea6dac84f0f9db2503d2812a101", + "rabbit_V.nog:md5,a57586e2151edc9054d42613c0f333ea", + "rabbit_V.nsd:md5,e90aab1550962796e8f4a74df53d681d", + "rabbit_V.nsi:md5,fc30fdc8baf22f8855ee54dc6fccf96a", + "rabbit_V.nsq:md5,6d4450cc6cdd47c35c383c105a2922f6", + "rabbit_V.phr:md5,3c4cac38b9a4a9d74eb5097745c82f2a", + "rabbit_V.pin:md5,78b0eead25d92252420ae988a057977a", + "rabbit_V.pog:md5,a57586e2151edc9054d42613c0f333ea", + "rabbit_V.psd:md5,e90aab1550962796e8f4a74df53d681d", + "rabbit_V.psi:md5,fc30fdc8baf22f8855ee54dc6fccf96a", + "rabbit_V.psq:md5,4223f96b39e2919008bf46ebf4bc8086", + "rat.ndm.imgt:md5,7317c7d30271cf5eb55dcaaa8d21d08f", + "rat.ndm.kabat:md5,2fd65f271ac90dc2f845053a18bc8136", + "rat.pdm.imgt:md5,6df63cc9e6531a29a592078e26178def", + "rat.pdm.kabat:md5,99996aab7e318763d2f5b3cf45a01c3d", + "rat_V.nhr:md5,bd4c6684859c91444a2ec36f50ce19be", + "rat_V.nin:md5,dd19ca8cd6641846a73681f00590c58e", + "rat_V.nog:md5,11b45f728cd8e07aac3bcd2e0118a114", + "rat_V.nsd:md5,f7c62ad597376b7e4aeba5539fea1947", + "rat_V.nsi:md5,1dca7089ad10f865f24d0c460548e4eb", + "rat_V.nsq:md5,08a7b14ce61dab2dfc980e37511ffdba", + "rat_V.phr:md5,10dde83b2bcc323c1f594cd2cf1943db", + "rat_V.pin:md5,f637df718130398afe844085dbe00e61", + "rat_V.pog:md5,11b45f728cd8e07aac3bcd2e0118a114", + "rat_V.psd:md5,f7c62ad597376b7e4aeba5539fea1947", + "rat_V.psi:md5,1dca7089ad10f865f24d0c460548e4eb", + "rat_V.psq:md5,7afff0d34e3ac4ce5e27ffcca802f167", + "readme:md5,a8da9737a87ea30634d9c76daff9e3a7", + "Entries:md5,637aaed90638717490c792d7db1380ad", + "Repository:md5,e7f792f89c1401fef550063f8ee5e7c8", + "Root:md5,064d27aa012c3bdd8b586bdfa152ae85", + "rhesus_monkey.ndm.imgt:md5,66c289aefc8d7fddf9bf4c9fa34e5f5b", + "rhesus_monkey.ndm.kabat:md5,5f13f6532cb44ae9049e04d108a32b9d", + "rhesus_monkey.pdm.imgt:md5,81629757b65a58851db23647cc6e130c", + "rhesus_monkey.pdm.kabat:md5,c3be9bef7c01b976419fa29121f12b08", + "rhesus_monkey_D.nhr:md5,5dbd53d004414cf37936705f0091f80b", + "rhesus_monkey_D.nin:md5,497cb469125caec99387cc30c244ed7f", + "rhesus_monkey_D.nog:md5,8c329c52cf5919b234d822f23e3ffeae", + "rhesus_monkey_D.nsd:md5,421c91caee071b623b25caaa5d37d56b", + "rhesus_monkey_D.nsi:md5,3b0f500e9d51c4a5b25897462b4d3769", + "rhesus_monkey_D.nsq:md5,1280769a0559128141088ee02864674b", + "rhesus_monkey_J.nhr:md5,28e5129ca9c6f265cdc2722615fc8846", + "rhesus_monkey_J.nin:md5,0717ec6ff45f06b9d3d22b7bb128dcab", + "rhesus_monkey_J.nog:md5,efc67de033c690611bd5b79b620b00da", + "rhesus_monkey_J.nsd:md5,7d90a63a1b7018a694412a1002a66418", + "rhesus_monkey_J.nsi:md5,b176549a4f1046e883bdfd236e7d3c09", + "rhesus_monkey_J.nsq:md5,a6f699c77221eaa00558b9c4a59ff7d7", + "rhesus_monkey_V.nhr:md5,0d6c4ea2e7c48cacaaae03f1d33ac0cf", + "rhesus_monkey_V.nin:md5,19c96733bfb8de3b6a177541cae21ed6", + "rhesus_monkey_V.nog:md5,1f06eac1e426e1fcf1d8cb865d5ef73b", + "rhesus_monkey_V.nsd:md5,b5b2ca588d397badadac3545ab123524", + "rhesus_monkey_V.nsi:md5,e0d3641d1bf83271d1da0316304b6185", + "rhesus_monkey_V.nsq:md5,313784b20eac86058819a7454801cafe", + "rhesus_monkey_V.phr:md5,0f6ef1c769c62ef1b782e748fcdda6e0", + "rhesus_monkey_V.pin:md5,f275f17c6893512860ba23c66e87d865", + "rhesus_monkey_V.pog:md5,1f06eac1e426e1fcf1d8cb865d5ef73b", + "rhesus_monkey_V.psd:md5,b5b2ca588d397badadac3545ab123524", + "rhesus_monkey_V.psi:md5,e0d3641d1bf83271d1da0316304b6185", + "rhesus_monkey_V.psq:md5,75030219251f33c6296959efaaa24c2f", + "human_gl.aux:md5,5801b62a007c5d98501116d8b6a7dde7", + "human_gl.aux.testonly:md5,b51b2475f3366e8e01a433149341d730", + "mouse_gl.aux:md5,8da2b395709c472408f1f7900a72e986", + "rabbit_gl.aux:md5,c14ec0d70f8fb8274f04521e684579c6", + "rat_gl.aux:md5,8c293acaa9173e734dc99cf32115d5c3", + "readme:md5,a8da9737a87ea30634d9c76daff9e3a7", + "rhesus_monkey_gl.aux:md5,92d38df5fe92bf01ff82beb62ec8e43d" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2025-12-09T10:08:33.373288" + }, + "test curlAndExtract with type - tar.gzip file": { + "content": [ + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2025-12-08T23:27:19.495861" + }, + "test curlAndExtract with type - tbzip2 file": { + "content": [ + [ + "CARD-Download-README.txt:md5,b57364cc1a5fab0541e13a01fabe5dea", + "PMID.tsv:md5,e3ce79c4b5dcf0a9e3117ed683f96e54", + "aro_categories.tsv:md5,6f9c4b0410b9e2b3cf5867a2a3f1db07", + "aro_categories_index.tsv:md5,d5fbc673c0de6601b07c8016b3909f8e", + "aro_index.tsv:md5,0f183c7869876fa32c8f86aade0df7b5", + "card.json:md5,72156d00155f69e637664bfb5d3b5395", + "nucleotide_fasta_protein_homolog_model.fasta:md5,696d1aa4f04bd08fc4bdeea33ab9db43", + "nucleotide_fasta_protein_knockout_model.fasta:md5,d8224ce019ad69a041d83ccf7877b4e0", + "nucleotide_fasta_protein_overexpression_model.fasta:md5,80a1e7957c79d311446e06c6dd49db8e", + "nucleotide_fasta_protein_variant_model.fasta:md5,7450e559045c9d1d8f13c73054c64f4c", + "nucleotide_fasta_rRNA_gene_variant_model.fasta:md5,bd53f46d630f652c9f6b7584c2126e1f", + "protein_fasta_protein_homolog_model.fasta:md5,36ea300133fd7c5a45de2fee4c5050bf", + "protein_fasta_protein_knockout_model.fasta:md5,f16667df70d1a5f910d3ae45f5250c3d", + "protein_fasta_protein_overexpression_model.fasta:md5,723e8762be5c96aed8c379a6499cecee", + "protein_fasta_protein_variant_model.fasta:md5,8c02d8fc84c9a90953f8534355244019", + "shortname_antibiotics.tsv:md5,9a4ba742fd8a3a49c7f50744001a4129", + "shortname_pathogens.tsv:md5,5211712be4f4c3306cbe4052cafae1d7", + "snps.txt:md5,529d4fdb74c8940c0930ec1a7a6d4980" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2025-12-09T11:01:00.867726" + }, + "test curlAndExtract with type - zip file": { + "content": [ + [ + "ncbi.map:md5,de30dbba85f9070612b632e2a5a95952", + "ncbi.tre:md5,4029dd2091c685b9a86ddd9d0d870db0" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.2" + }, + "timestamp": "2025-12-08T23:32:07.753491" + }, + "test curlAndExtract - tar file": { + "content": [ + [ + "airr_c_human.tar:md5,a29a0c8d1520ff884e873d9a114684f6", + "airr_c_mouse.tar:md5,b46a8b195eb6d15ed3f84fc51434d126", + 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