From 0cbd5c00cba5af246c5669e26df8bc6cf0f319dc Mon Sep 17 00:00:00 2001 From: CI Date: Thu, 20 Mar 2025 20:00:43 +0000 Subject: [PATCH] Build branch v0.3 with version v0.3.6 (3a985c8) Build pipeline: viash-hub.demultiplex.v0.3-2vbxf Source commit: https://github.com/viash-hub/demultiplex/commit/3a985c83869bcd78ba6d325f1a817514b52a132a Source message: Bump version to v0.3.6 --- CHANGELOG.md | 6 ++++++ _viash.yaml | 2 +- src/dataflow/gather_fastqs_and_validate/main.nf | 4 ++-- .../io/interop_summary_to_csv/.config.vsh.yaml | 12 ++++++------ .../interop_summary_to_csv | 14 +++++++------- target/executable/io/publish/.config.vsh.yaml | 12 ++++++------ target/executable/io/publish/publish | 14 +++++++------- target/executable/io/untar/.config.vsh.yaml | 12 ++++++------ target/executable/io/untar/untar | 14 +++++++------- .../dataflow/combine_samples/.config.vsh.yaml | 10 +++++----- target/nextflow/dataflow/combine_samples/main.nf | 12 ++++++------ .../dataflow/combine_samples/nextflow.config | 2 +- .../gather_fastqs_and_validate/.config.vsh.yaml | 10 +++++----- .../dataflow/gather_fastqs_and_validate/main.nf | 16 ++++++++-------- .../gather_fastqs_and_validate/nextflow.config | 2 +- target/nextflow/demultiplex/.config.vsh.yaml | 10 +++++----- target/nextflow/demultiplex/main.nf | 12 ++++++------ target/nextflow/demultiplex/nextflow.config | 2 +- .../io/interop_summary_to_csv/.config.vsh.yaml | 12 ++++++------ .../nextflow/io/interop_summary_to_csv/main.nf | 16 ++++++++-------- .../io/interop_summary_to_csv/nextflow.config | 2 +- target/nextflow/io/publish/.config.vsh.yaml | 12 ++++++------ target/nextflow/io/publish/main.nf | 16 ++++++++-------- target/nextflow/io/publish/nextflow.config | 2 +- target/nextflow/io/untar/.config.vsh.yaml | 12 ++++++------ target/nextflow/io/untar/main.nf | 16 ++++++++-------- target/nextflow/io/untar/nextflow.config | 2 +- target/nextflow/runner/.config.vsh.yaml | 10 +++++----- target/nextflow/runner/main.nf | 12 ++++++------ target/nextflow/runner/nextflow.config | 2 +- 30 files changed, 143 insertions(+), 137 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74e02b3..960ad4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,3 +1,9 @@ +# demultiplex v0.3.6 + +## Minor updates + +* Allow letter case variants for headers when looking for sample information in run information CSV (PR #38). + # demultiplex v0.3.5 ## Breaking changes diff --git a/_viash.yaml b/_viash.yaml index 96ed8ec..ff7aa32 100644 --- a/_viash.yaml +++ b/_viash.yaml @@ -1,5 +1,5 @@ name: demultiplex -version: v0.3.5 +version: v0.3.6 description: | Demultiplexing pipeline license: MIT diff --git a/src/dataflow/gather_fastqs_and_validate/main.nf b/src/dataflow/gather_fastqs_and_validate/main.nf index 76c5d60..98ee102 100644 --- a/src/dataflow/gather_fastqs_and_validate/main.nf +++ b/src/dataflow/gather_fastqs_and_validate/main.nf @@ -30,8 +30,8 @@ workflow run_wf { return true } // [Data], [BCLConvert_Data] for illumina - // [Samples] for Element Biosciences - if (header in ["Data", "Samples", "BCLConvert_Data"]) { + // [Samples] or sometimes [SAMPLES] for Element Biosciences + if (header.toLowerCase() in ["data", "samples", "bclconvert_data"]) { println "Found header [${header}], start parsing." start_parsing = true return diff --git a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml index 14df06f..3971964 100644 --- a/target/executable/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/executable/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -146,12 +146,12 @@ build_info: output: "target/executable/io/interop_summary_to_csv" executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv index 9394abd..3f17559 100755 --- a/target/executable/io/interop_summary_to_csv/interop_summary_to_csv +++ b/target/executable/io/interop_summary_to_csv/interop_summary_to_csv @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# interop_summary_to_csv v0.3.5 +# interop_summary_to_csv v0.3.6 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "interop_summary_to_csv v0.3.5" + echo "interop_summary_to_csv v0.3.6" echo "" echo "Input arguments:" echo " --input" @@ -470,10 +470,10 @@ tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \ mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/ LABEL org.opencontainers.image.description="Companion container for running component io interop_summary_to_csv" -LABEL org.opencontainers.image.created="2025-03-04T13:21:45Z" +LABEL org.opencontainers.image.created="2025-03-20T19:41:31Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484" -LABEL org.opencontainers.image.version="v0.3.5" +LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a" +LABEL org.opencontainers.image.version="v0.3.6" VIASHDOCKER fi @@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "interop_summary_to_csv v0.3.5" + echo "interop_summary_to_csv v0.3.6" exit ;; --input) @@ -733,7 +733,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/interop_summary_to_csv:v0.3.6' fi # print dockerfile diff --git a/target/executable/io/publish/.config.vsh.yaml b/target/executable/io/publish/.config.vsh.yaml index 298a6d1..cc3142d 100644 --- a/target/executable/io/publish/.config.vsh.yaml +++ b/target/executable/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -178,7 +178,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -196,12 +196,12 @@ build_info: output: "target/executable/io/publish" executable: "target/executable/io/publish/publish" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/publish/publish b/target/executable/io/publish/publish index 9a22005..cdb673f 100755 --- a/target/executable/io/publish/publish +++ b/target/executable/io/publish/publish @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# publish v0.3.5 +# publish v0.3.6 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "publish v0.3.5" + echo "publish v0.3.6" echo "" echo "Publish the processed results of the run" echo "" @@ -490,10 +490,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io publish" -LABEL org.opencontainers.image.created="2025-03-04T13:21:46Z" +LABEL org.opencontainers.image.created="2025-03-20T19:41:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484" -LABEL org.opencontainers.image.version="v0.3.5" +LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a" +LABEL org.opencontainers.image.version="v0.3.6" VIASHDOCKER fi @@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "publish v0.3.5" + echo "publish v0.3.6" exit ;; --input) @@ -814,7 +814,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/publish:v0.3.6' fi # print dockerfile diff --git a/target/executable/io/untar/.config.vsh.yaml b/target/executable/io/untar/.config.vsh.yaml index 7e78a82..5b00547 100644 --- a/target/executable/io/untar/.config.vsh.yaml +++ b/target/executable/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -153,12 +153,12 @@ build_info: output: "target/executable/io/untar" executable: "target/executable/io/untar/untar" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -174,7 +174,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/executable/io/untar/untar b/target/executable/io/untar/untar index b1bde25..3de00b3 100755 --- a/target/executable/io/untar/untar +++ b/target/executable/io/untar/untar @@ -1,6 +1,6 @@ #!/usr/bin/env bash -# untar v0.3.5 +# untar v0.3.6 # # This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP" # ViashHelp: Display helpful explanation about this executable function ViashHelp { - echo "untar v0.3.5" + echo "untar v0.3.6" echo "" echo "Unpack a .tar file. When the contents of the .tar file is just a single" echo "directory," @@ -476,10 +476,10 @@ RUN apt-get update && \ rm -rf /var/lib/apt/lists/* LABEL org.opencontainers.image.description="Companion container for running component io untar" -LABEL org.opencontainers.image.created="2025-03-04T13:21:46Z" +LABEL org.opencontainers.image.created="2025-03-20T19:41:30Z" LABEL org.opencontainers.image.source="https://github.com/viash-hub/demultiplex" -LABEL org.opencontainers.image.revision="18e092d169cc2704a2e4e705485d9231911d0484" -LABEL org.opencontainers.image.version="v0.3.5" +LABEL org.opencontainers.image.revision="3a985c83869bcd78ba6d325f1a817514b52a132a" +LABEL org.opencontainers.image.version="v0.3.6" VIASHDOCKER fi @@ -615,7 +615,7 @@ while [[ $# -gt 0 ]]; do shift 1 ;; --version) - echo "untar v0.3.5" + echo "untar v0.3.6" exit ;; --input) @@ -745,7 +745,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then # determine docker image id if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then - VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.5' + VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/demultiplex/io/untar:v0.3.6' fi # print dockerfile diff --git a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml index b62a3a0..cce531f 100644 --- a/target/nextflow/dataflow/combine_samples/.config.vsh.yaml +++ b/target/nextflow/dataflow/combine_samples/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "combine_samples" namespace: "dataflow" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -162,12 +162,12 @@ build_info: output: "target/nextflow/dataflow/combine_samples" executable: "target/nextflow/dataflow/combine_samples/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -183,7 +183,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/combine_samples/main.nf b/target/nextflow/dataflow/combine_samples/main.nf index 41bd72e..d3fcb3a 100644 --- a/target/nextflow/dataflow/combine_samples/main.nf +++ b/target/nextflow/dataflow/combine_samples/main.nf @@ -1,4 +1,4 @@ -// combine_samples v0.3.5 +// combine_samples v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "combine_samples", "namespace" : "dataflow", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3000,13 +3000,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/combine_samples", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3023,7 +3023,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/dataflow/combine_samples/nextflow.config b/target/nextflow/dataflow/combine_samples/nextflow.config index 2f6a3e9..9c6c989 100644 --- a/target/nextflow/dataflow/combine_samples/nextflow.config +++ b/target/nextflow/dataflow/combine_samples/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/combine_samples' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.' } diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml index c441c9c..71f648d 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "gather_fastqs_and_validate" namespace: "dataflow" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -138,12 +138,12 @@ build_info: output: "target/nextflow/dataflow/gather_fastqs_and_validate" executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -159,7 +159,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf index deced8f..47176b2 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/main.nf @@ -1,4 +1,4 @@ -// gather_fastqs_and_validate v0.3.5 +// gather_fastqs_and_validate v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "gather_fastqs_and_validate", "namespace" : "dataflow", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -2973,13 +2973,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/dataflow/gather_fastqs_and_validate", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -2996,7 +2996,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", @@ -3051,8 +3051,8 @@ workflow run_wf { return true } // [Data], [BCLConvert_Data] for illumina - // [Samples] for Element Biosciences - if (header in ["Data", "Samples", "BCLConvert_Data"]) { + // [Samples] or sometimes [SAMPLES] for Element Biosciences + if (header.toLowerCase() in ["data", "samples", "bclconvert_data"]) { println "Found header [${header}], start parsing." start_parsing = true return diff --git a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config index cb4b69a..01488ca 100644 --- a/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config +++ b/target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'dataflow/gather_fastqs_and_validate' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n' } diff --git a/target/nextflow/demultiplex/.config.vsh.yaml b/target/nextflow/demultiplex/.config.vsh.yaml index 9512eee..430c215 100644 --- a/target/nextflow/demultiplex/.config.vsh.yaml +++ b/target/nextflow/demultiplex/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "demultiplex" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -244,9 +244,9 @@ build_info: output: "target/nextflow/demultiplex" executable: "target/nextflow/demultiplex/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" dependencies: - "target/nextflow/io/untar" - "target/nextflow/dataflow/gather_fastqs_and_validate" @@ -258,7 +258,7 @@ build_info: - "target/dependencies/vsh/vsh/biobox/v0.3.0/nextflow/multiqc" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -274,7 +274,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/demultiplex/main.nf b/target/nextflow/demultiplex/main.nf index e46d2c7..303c414 100644 --- a/target/nextflow/demultiplex/main.nf +++ b/target/nextflow/demultiplex/main.nf @@ -1,4 +1,4 @@ -// demultiplex v0.3.5 +// demultiplex v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3120,13 +3120,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/demultiplex", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3143,7 +3143,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/demultiplex/nextflow.config b/target/nextflow/demultiplex/nextflow.config index 6a01b6b..e0e5fc5 100644 --- a/target/nextflow/demultiplex/nextflow.config +++ b/target/nextflow/demultiplex/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'demultiplex' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'Demultiplexing of raw sequencing data' } diff --git a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml index a215ab3..0d01f66 100644 --- a/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml +++ b/target/nextflow/io/interop_summary_to_csv/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "interop_summary_to_csv" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -121,7 +121,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -146,12 +146,12 @@ build_info: output: "target/nextflow/io/interop_summary_to_csv" executable: "target/nextflow/io/interop_summary_to_csv/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -167,7 +167,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/interop_summary_to_csv/main.nf b/target/nextflow/io/interop_summary_to_csv/main.nf index 177c019..916a825 100644 --- a/target/nextflow/io/interop_summary_to_csv/main.nf +++ b/target/nextflow/io/interop_summary_to_csv/main.nf @@ -1,4 +1,4 @@ -// interop_summary_to_csv v0.3.5 +// interop_summary_to_csv v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "interop_summary_to_csv", "namespace" : "io", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -2955,7 +2955,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.5", + "target_tag" : "v0.3.6", "namespace_separator" : "/", "setup" : [ { @@ -2985,13 +2985,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/interop_summary_to_csv", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3008,7 +3008,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", @@ -3431,7 +3431,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/interop_summary_to_csv", - "tag" : "v0.3.5" + "tag" : "v0.3.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/interop_summary_to_csv/nextflow.config b/target/nextflow/io/interop_summary_to_csv/nextflow.config index a8d053f..5b263c0 100644 --- a/target/nextflow/io/interop_summary_to_csv/nextflow.config +++ b/target/nextflow/io/interop_summary_to_csv/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/interop_summary_to_csv' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' } process.container = 'nextflow/bash:latest' diff --git a/target/nextflow/io/publish/.config.vsh.yaml b/target/nextflow/io/publish/.config.vsh.yaml index 6668cdf..3e39f86 100644 --- a/target/nextflow/io/publish/.config.vsh.yaml +++ b/target/nextflow/io/publish/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "publish" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -178,7 +178,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -196,12 +196,12 @@ build_info: output: "target/nextflow/io/publish" executable: "target/nextflow/io/publish/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -217,7 +217,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/publish/main.nf b/target/nextflow/io/publish/main.nf index 36db6bb..eeb3498 100644 --- a/target/nextflow/io/publish/main.nf +++ b/target/nextflow/io/publish/main.nf @@ -1,4 +1,4 @@ -// publish v0.3.5 +// publish v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "publish", "namespace" : "io", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3021,7 +3021,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.5", + "target_tag" : "v0.3.6", "namespace_separator" : "/", "setup" : [ { @@ -3044,13 +3044,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/publish", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3067,7 +3067,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", @@ -3518,7 +3518,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/publish", - "tag" : "v0.3.5" + "tag" : "v0.3.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/publish/nextflow.config b/target/nextflow/io/publish/nextflow.config index 3f68011..0f373b1 100644 --- a/target/nextflow/io/publish/nextflow.config +++ b/target/nextflow/io/publish/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/publish' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'Publish the processed results of the run' } diff --git a/target/nextflow/io/untar/.config.vsh.yaml b/target/nextflow/io/untar/.config.vsh.yaml index 1c55be9..b17cbc8 100644 --- a/target/nextflow/io/untar/.config.vsh.yaml +++ b/target/nextflow/io/untar/.config.vsh.yaml @@ -1,6 +1,6 @@ name: "untar" namespace: "io" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -135,7 +135,7 @@ engines: id: "docker" image: "debian:stable-slim" target_registry: "images.viash-hub.com" - target_tag: "v0.3.5" + target_tag: "v0.3.6" namespace_separator: "/" setup: - type: "apt" @@ -153,12 +153,12 @@ build_info: output: "target/nextflow/io/untar" executable: "target/nextflow/io/untar/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -174,7 +174,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/io/untar/main.nf b/target/nextflow/io/untar/main.nf index 8db1249..06c9c8f 100644 --- a/target/nextflow/io/untar/main.nf +++ b/target/nextflow/io/untar/main.nf @@ -1,4 +1,4 @@ -// untar v0.3.5 +// untar v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2806,7 +2806,7 @@ meta = [ "config": processConfig(readJsonBlob('''{ "name" : "untar", "namespace" : "io", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -2974,7 +2974,7 @@ meta = [ "id" : "docker", "image" : "debian:stable-slim", "target_registry" : "images.viash-hub.com", - "target_tag" : "v0.3.5", + "target_tag" : "v0.3.6", "namespace_separator" : "/", "setup" : [ { @@ -2997,13 +2997,13 @@ meta = [ "engine" : "docker|native", "output" : "target/nextflow/io/untar", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3020,7 +3020,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", @@ -3473,7 +3473,7 @@ meta["defaults"] = [ "container" : { "registry" : "images.viash-hub.com", "image" : "vsh/demultiplex/io/untar", - "tag" : "v0.3.5" + "tag" : "v0.3.6" }, "tag" : "$id" }'''), diff --git a/target/nextflow/io/untar/nextflow.config b/target/nextflow/io/untar/nextflow.config index a529d29..9eeb5d4 100644 --- a/target/nextflow/io/untar/nextflow.config +++ b/target/nextflow/io/untar/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'io/untar' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n' } diff --git a/target/nextflow/runner/.config.vsh.yaml b/target/nextflow/runner/.config.vsh.yaml index 71cb683..e45e6fe 100644 --- a/target/nextflow/runner/.config.vsh.yaml +++ b/target/nextflow/runner/.config.vsh.yaml @@ -1,5 +1,5 @@ name: "runner" -version: "v0.3.5" +version: "v0.3.6" argument_groups: - name: "Input arguments" arguments: @@ -192,15 +192,15 @@ build_info: output: "target/nextflow/runner" executable: "target/nextflow/runner/main.nf" viash_version: "0.9.0" - git_commit: "18e092d169cc2704a2e4e705485d9231911d0484" + git_commit: "3a985c83869bcd78ba6d325f1a817514b52a132a" git_remote: "https://github.com/viash-hub/demultiplex" - git_tag: "v0.3.4-6-g18e092d" + git_tag: "v0.3.5-3-g3a985c8" dependencies: - "target/nextflow/demultiplex" - "target/nextflow/io/publish" package_config: name: "demultiplex" - version: "v0.3.5" + version: "v0.3.6" description: "Demultiplexing pipeline\n" info: test_resources: @@ -216,7 +216,7 @@ package_config: )'\n" - ".engines += { type: \"native\" }" - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'" - - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + - ".engines[.type == 'docker'].target_tag := 'v0.3.6'" keywords: - "bioinformatics" - "sequence" diff --git a/target/nextflow/runner/main.nf b/target/nextflow/runner/main.nf index 874a963..1bdd3cb 100644 --- a/target/nextflow/runner/main.nf +++ b/target/nextflow/runner/main.nf @@ -1,4 +1,4 @@ -// runner v0.3.5 +// runner v0.3.6 // // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data @@ -2805,7 +2805,7 @@ meta = [ "resources_dir": moduleDir.toRealPath().normalize(), "config": processConfig(readJsonBlob('''{ "name" : "runner", - "version" : "v0.3.5", + "version" : "v0.3.6", "argument_groups" : [ { "name" : "Input arguments", @@ -3040,13 +3040,13 @@ meta = [ "engine" : "native|native", "output" : "target/nextflow/runner", "viash_version" : "0.9.0", - "git_commit" : "18e092d169cc2704a2e4e705485d9231911d0484", + "git_commit" : "3a985c83869bcd78ba6d325f1a817514b52a132a", "git_remote" : "https://github.com/viash-hub/demultiplex", - "git_tag" : "v0.3.4-6-g18e092d" + "git_tag" : "v0.3.5-3-g3a985c8" }, "package_config" : { "name" : "demultiplex", - "version" : "v0.3.5", + "version" : "v0.3.6", "description" : "Demultiplexing pipeline\n", "info" : { "test_resources" : [ @@ -3063,7 +3063,7 @@ meta = [ ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].directives.tag := '$id'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n", ".engines += { type: \\"native\\" }", ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'", - ".engines[.type == 'docker'].target_tag := 'v0.3.5'" + ".engines[.type == 'docker'].target_tag := 'v0.3.6'" ], "keywords" : [ "bioinformatics", diff --git a/target/nextflow/runner/nextflow.config b/target/nextflow/runner/nextflow.config index ef2b7ca..5eff28c 100644 --- a/target/nextflow/runner/nextflow.config +++ b/target/nextflow/runner/nextflow.config @@ -2,7 +2,7 @@ manifest { name = 'runner' mainScript = 'main.nf' nextflowVersion = '!>=20.12.1-edge' - version = 'v0.3.5' + version = 'v0.3.6' description = 'Runner for demultiplexing of raw sequencing data' }