From 8cc89f482362918bb6c1c90f220817a2125a0c4c Mon Sep 17 00:00:00 2001 From: labkey-jeckels Date: Mon, 16 Dec 2024 18:11:09 -0800 Subject: [PATCH] Import results directory too --- .../org/labkey/nextflow/pipeline/NextFlowPipelineJob.java | 6 ++++-- .../src/org/labkey/nextflow/pipeline/NextFlowProtocol.java | 2 +- .../src/org/labkey/nextflow/pipeline/NextFlowRunTask.java | 1 + 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java index 40455d8c..1cc4d8c3 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java @@ -70,9 +70,12 @@ private static Path createConfig(Path configTemplate, Path parentDir, Path jobDi String webdavUrl = FileContentService.get().getWebDavUrl(parentDir, container, FileContentService.PathType.full); webdavUrl = StringUtils.stripEnd(webdavUrl, "/"); - String substitutedContent = template.replace("${quant_spectra_dir}", "quant_spectra_dir = '" + webdavUrl + "'"); + String uploadUrl = FileContentService.get().getWebDavUrl(jobDir, container, FileContentService.PathType.full); + uploadUrl = StringUtils.stripEnd(uploadUrl, "/"); + substitutedContent = substitutedContent.replace("${panorama.upload_url}", "panorama.upload_url = '" + uploadUrl + "'"); + Path substitutedFile = jobDir.resolve(configTemplate.getFileName()); try (BufferedWriter writer = Files.newBufferedWriter(substitutedFile)) { @@ -116,5 +119,4 @@ public File findOutputFile(String name) { return null; } - } diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java index a2d7270c..2faf82b1 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowProtocol.java @@ -16,7 +16,7 @@ public class NextFlowProtocol extends AbstractFileAnalysisProtocol { public static final List INPUT_TYPES = List.of( - new FileType(".RAW"), + new FileType(".raw"), new FileType(".mzML")); public NextFlowProtocol() diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java index 8954963e..35fcf5b1 100644 --- a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java +++ b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java @@ -80,6 +80,7 @@ public NextFlowRunTask(Factory factory, PipelineJob job) action.addInput(inputFile.toFile(), SPECTRA_INPUT_ROLE); } addOutputs(action, getJob().getLogFilePath().getParent().resolve("reports")); + addOutputs(action, getJob().getLogFilePath().getParent().resolve("results")); return new RecordedActionSet(action); } catch (IOException e)